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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (14) Show 14 proteins XML

Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2021-09-14 15:44:46 UTC

HMDB ID

HMDB0000767

Secondary Accession Numbers

HMDB0006075
HMDB00767
HMDB06075

Metabolite Identification

Common Name

Pseudouridine

Description

Pseudouridine, also known as psi-uridine or 5-ribosyluracil, belongs to the class of organic compounds known as nucleoside and nucleotide analogues. These are analogues of nucleosides and nucleotides, such as phosphonated nucleosides, C-glycosylated nucleoside bases, analogues where the sugar unit is a pyranose, and carbocyclic nucleosides. Pseudouridine specifically has its uracil attached via a carbon-carbon instead of a nitrogen-carbon glycosidic bond to the ribofuranose. It is the most prevalent of the over one hundred different modified nucleosides found in RNA (PMID: 17113994 ). Pseudouridine is a solid that is soluble in water. Pseudouridine exists in all living species, ranging from bacteria to humans, and is in all classes of RNA except mRNA. It is formed by enzymes called pseudouridine synthases, which post-transcriptionally isomerize specific uridine residues in RNA.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0000767
     RDKit          3D
Pseudouridine
 29 30  0  0  0  0  0  0  0  0999 V2000
    5.2921    0.8473   -0.2060 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0950    0.6308   -0.0231 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3482    0.2718   -1.0990 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0462    0.0268   -0.9396 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3716    0.1016    0.2418 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0429   -0.0569    0.3122 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9013    0.9019    0.7525 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0909    0.4202    0.0761 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3052    1.1916    0.3689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1776    2.4898   -0.0682 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1211   -1.0567    0.3815 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4275   -1.7430   -0.7857 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6846   -1.3399    0.7743 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1971   -2.5011    0.2675 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1523    0.4727    1.3443 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5215    0.5318    2.4190 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4524    0.7170    1.1919 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7737    0.1821   -2.0385 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5351   -0.2562   -1.8906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3479   -0.1035   -0.8578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8478    0.6018   -1.0201 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1659    0.7419   -0.1521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5388    1.2723    1.4624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2447    2.7491   -0.2739 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8428   -1.2998    1.2044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6660   -2.6930   -0.5757 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7381   -1.3485    1.9117 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7113   -2.7174    0.6563 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0409    0.9657    2.0269 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
  5 15  1  0
 15 16  2  0
 15 17  1  0
 17  2  1  0
 13  6  1  0
  3 18  1  0
  4 19  1  0
  6 20  1  6
  8 21  1  6
  9 22  1  0
  9 23  1  0
 10 24  1  0
 11 25  1  1
 12 26  1  0
 13 27  1  1
 14 28  1  0
 17 29  1  0
M  END


  Mrv1652309042000062D          

 17 18  0  0  1  0            999 V2000
    0.0000   -0.8436    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.3938    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.3938    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8064    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6686    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6674   -2.1536    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6674   -2.1536    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4125   -2.9382    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4125   -2.9382    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4521   -1.8986    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.8436    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8974   -3.6056    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6314    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8974   -3.6056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5619   -4.3593    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  7  1  1  1  0  0  0
  1  2  1  0  0  0  0
  2 13  2  0  0  0  0
  1  3  2  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  4  6  1  0  0  0  0
  6 15  2  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 11  1  0  0  0  0
  9 12  1  6  0  0  0
 10 16  1  1  0  0  0
 10 11  1  0  0  0  0
 11 14  1  6  0  0  0
 16 17  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000767

> <DATABASE_NAME>
hmdb

> <SMILES>
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)C1=CNC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H12N2O6/c12-2-4-5(13)6(14)7(17-4)3-1-10-9(16)11-8(3)15/h1,4-7,12-14H,2H2,(H2,10,11,15,16)/t4-,5-,6-,7+/m1/s1

> <INCHI_KEY>
PTJWIQPHWPFNBW-GBNDHIKLSA-N

> <FORMULA>
C9H12N2O6

> <MOLECULAR_WEIGHT>
244.2014

> <EXACT_MASS>
244.069536126

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
21.794147572683546

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
-2.01

> <JCHEM_LOGP>
-3.1001478630000006

> <ALOGPS_LOGS>
-0.58

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.602908039116013

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.663736427830294

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9792001006523368

> <JCHEM_POLAR_SURFACE_AREA>
128.12

> <JCHEM_REFRACTIVITY>
52.44100000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.38e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
β-pseudouridine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0000767
     RDKit          3D
Pseudouridine
 29 30  0  0  0  0  0  0  0  0999 V2000
    5.2921    0.8473   -0.2060 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0950    0.6308   -0.0231 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3482    0.2718   -1.0990 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0462    0.0268   -0.9396 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3716    0.1016    0.2418 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0429   -0.0569    0.3122 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9013    0.9019    0.7525 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0909    0.4202    0.0761 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3052    1.1916    0.3689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1776    2.4898   -0.0682 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1211   -1.0567    0.3815 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4275   -1.7430   -0.7857 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6846   -1.3399    0.7743 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1971   -2.5011    0.2675 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1523    0.4727    1.3443 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5215    0.5318    2.4190 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4524    0.7170    1.1919 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7737    0.1821   -2.0385 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5351   -0.2562   -1.8906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3479   -0.1035   -0.8578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8478    0.6018   -1.0201 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1659    0.7419   -0.1521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5388    1.2723    1.4624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2447    2.7491   -0.2739 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8428   -1.2998    1.2044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6660   -2.6930   -0.5757 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7381   -1.3485    1.9117 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7113   -2.7174    0.6563 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0409    0.9657    2.0269 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
  5 15  1  0
 15 16  2  0
 15 17  1  0
 17  2  1  0
 13  6  1  0
  3 18  1  0
  4 19  1  0
  6 20  1  6
  8 21  1  6
  9 22  1  0
  9 23  1  0
 10 24  1  0
 11 25  1  1
 12 26  1  0
 13 27  1  1
 14 28  1  0
 17 29  1  0
M  END

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0       0.000  -1.575   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -0.805   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334  -0.805   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       1.334   0.735   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0      -1.334   0.735   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       0.000   1.505   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000  -3.115   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.246  -4.020   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.246  -4.020   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.770  -5.485   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.770  -5.485   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       2.711  -3.544   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       2.667  -1.575   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       1.675  -6.730   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.000   3.045   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -1.675  -6.730   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -1.049  -8.137   0.000  0.00  0.00           O+0
CONECT    1    7    2    3                                                  
CONECT    2    1   13    4                                                  
CONECT    3    1    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    6                                                       
CONECT    6    5    4   15                                                  
CONECT    7    1    8    9                                                  
CONECT    8    7   10                                                       
CONECT    9    7   11   12                                                  
CONECT   10    8   16   11                                                  
CONECT   11    9   10   14                                                  
CONECT   12    9                                                            
CONECT   13    2                                                            
CONECT   14   11                                                            
CONECT   15    6                                                            
CONECT   16   10   17                                                       
CONECT   17   16                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

COMPND    HMDB0000767
HETATM    1  O1  UNL     1       5.292   0.847  -0.206  1.00  0.00           O  
HETATM    2  C1  UNL     1       4.095   0.631  -0.023  1.00  0.00           C  
HETATM    3  N1  UNL     1       3.348   0.272  -1.099  1.00  0.00           N  
HETATM    4  C2  UNL     1       2.046   0.027  -0.940  1.00  0.00           C  
HETATM    5  C3  UNL     1       1.372   0.102   0.242  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.043  -0.057   0.312  1.00  0.00           C  
HETATM    7  O2  UNL     1      -0.901   0.902   0.752  1.00  0.00           O  
HETATM    8  C5  UNL     1      -2.091   0.420   0.076  1.00  0.00           C  
HETATM    9  C6  UNL     1      -3.305   1.192   0.369  1.00  0.00           C  
HETATM   10  O3  UNL     1      -3.178   2.490  -0.068  1.00  0.00           O  
HETATM   11  C7  UNL     1      -2.121  -1.057   0.382  1.00  0.00           C  
HETATM   12  O4  UNL     1      -2.428  -1.743  -0.786  1.00  0.00           O  
HETATM   13  C8  UNL     1      -0.685  -1.340   0.774  1.00  0.00           C  
HETATM   14  O5  UNL     1      -0.197  -2.501   0.267  1.00  0.00           O  
HETATM   15  C9  UNL     1       2.152   0.473   1.344  1.00  0.00           C  
HETATM   16  O6  UNL     1       1.521   0.532   2.419  1.00  0.00           O  
HETATM   17  N2  UNL     1       3.452   0.717   1.192  1.00  0.00           N  
HETATM   18  H1  UNL     1       3.774   0.182  -2.038  1.00  0.00           H  
HETATM   19  H2  UNL     1       1.535  -0.256  -1.891  1.00  0.00           H  
HETATM   20  H3  UNL     1      -0.348  -0.103  -0.858  1.00  0.00           H  
HETATM   21  H4  UNL     1      -1.848   0.602  -1.020  1.00  0.00           H  
HETATM   22  H5  UNL     1      -4.166   0.742  -0.152  1.00  0.00           H  
HETATM   23  H6  UNL     1      -3.539   1.272   1.462  1.00  0.00           H  
HETATM   24  H7  UNL     1      -2.245   2.749  -0.274  1.00  0.00           H  
HETATM   25  H8  UNL     1      -2.843  -1.300   1.204  1.00  0.00           H  
HETATM   26  H9  UNL     1      -2.666  -2.693  -0.576  1.00  0.00           H  
HETATM   27  H10 UNL     1      -0.738  -1.348   1.912  1.00  0.00           H  
HETATM   28  H11 UNL     1       0.711  -2.717   0.656  1.00  0.00           H  
HETATM   29  H12 UNL     1       4.041   0.966   2.027  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   17
CONECT    3    4   18
CONECT    4    5    5   19
CONECT    5    6   15
CONECT    6    7   13   20
CONECT    7    8
CONECT    8    9   11   21
CONECT    9   10   22   23
CONECT   10   24
CONECT   11   12   13   25
CONECT   12   26
CONECT   13   14   27
CONECT   14   28
CONECT   15   16   16   17
CONECT   17   29
END

HMDB0000767
     RDKit          3D
Pseudouridine
 29 30  0  0  0  0  0  0  0  0999 V2000
    5.2921    0.8473   -0.2060 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0950    0.6308   -0.0231 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3482    0.2718   -1.0990 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0462    0.0268   -0.9396 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3716    0.1016    0.2418 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0429   -0.0569    0.3122 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9013    0.9019    0.7525 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0909    0.4202    0.0761 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3052    1.1916    0.3689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1776    2.4898   -0.0682 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1211   -1.0567    0.3815 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4275   -1.7430   -0.7857 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6846   -1.3399    0.7743 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1971   -2.5011    0.2675 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1523    0.4727    1.3443 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5215    0.5318    2.4190 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4524    0.7170    1.1919 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7737    0.1821   -2.0385 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5351   -0.2562   -1.8906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3479   -0.1035   -0.8578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8478    0.6018   -1.0201 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1659    0.7419   -0.1521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5388    1.2723    1.4624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2447    2.7491   -0.2739 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8428   -1.2998    1.2044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6660   -2.6930   -0.5757 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7381   -1.3485    1.9117 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7113   -2.7174    0.6563 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0409    0.9657    2.0269 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
  5 15  1  0
 15 16  2  0
 15 17  1  0
 17  2  1  0
 13  6  1  0
  3 18  1  0
  4 19  1  0
  6 20  1  6
  8 21  1  6
  9 22  1  0
  9 23  1  0
 10 24  1  0
 11 25  1  1
 12 26  1  0
 13 27  1  1
 14 28  1  0
 17 29  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
(1S)-1,4-Anhydro-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-ribitol	ChEBI
5-(beta-D-Ribofuranosyl)uracil	ChEBI
beta-Pseudouridine	ChEBI
p	ChEBI
Psi-uridine	ChEBI
5-(b-D-Ribofuranosyl)uracil	Generator
5-(Β-D-ribofuranosyl)uracil	Generator
b-Pseudouridine	Generator
Β-pseudouridine	Generator
5-(b-delta-Ribofuranosyl)uracil	HMDB
5-b-D-Ribofuranosyl-uracil	HMDB
5-beta-delta-Ribofuranosyl-uracil	HMDB
5-Ribosyluracil	HMDB
b-D-Pseudouridine	HMDB
beta-delta-Pseudouridine	HMDB
Pseudouridine C	HMDB
Y-uridine	HMDB
5-beta-D-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione	HMDB
5-Β-D-ribofuranosyl-2,4(1H,3H)-pyrimidinedione	HMDB
beta-D-Pseudouridine	HMDB
Β-D-pseudouridine	HMDB
Ψ-uridine	HMDB
Pseudouridine	HMDB

Chemical Formula

C₉H₁₂N₂O₆

Average Molecular Weight

244.2014

Monoisotopic Molecular Weight

244.069536126

IUPAC Name

5-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

β-pseudouridine

CAS Registry Number

1445-07-4

SMILES

OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)C1=CNC(=O)NC1=O

InChI Identifier

InChI=1S/C9H12N2O6/c12-2-4-5(13)6(14)7(17-4)3-1-10-9(16)11-8(3)15/h1,4-7,12-14H,2H2,(H2,10,11,15,16)/t4-,5-,6-,7+/m1/s1

InChI Key

PTJWIQPHWPFNBW-GBNDHIKLSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as nucleoside and nucleotide analogues. These are analogues of nucleosides and nucleotides. These include phosphonated nucleosides, C-glycosylated nucleoside bases, analogues where the sugar unit is a pyranose, and carbocyclic nucleosides, among others.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Nucleoside and nucleotide analogues

Sub Class

Not Available

Direct Parent

Nucleoside and nucleotide analogues

Alternative Parents

Substituents

C-glycosyl compound
Glycosyl compound
Pentose monosaccharide
Pyrimidone
Hydropyrimidine
Monosaccharide
Pyrimidine
Heteroaromatic compound
Tetrahydrofuran
Vinylogous amide
Lactam
Secondary alcohol
Urea
Azacycle
Oxacycle
Ether
Dialkyl ether
Organoheterocyclic compound
Primary alcohol
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic oxide
Alcohol
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pseudouridines (CHEBI:17802 )

Ontology

Not Available

Placenta (HMDB: HMDB0000767)

Biofluid or Excreta

Excreta

Urine (PMID: 15116424)
Feces (PMID: 27015276)

Non-excretory biofluid

Blood (PMID: 16139832)
Amniotic Fluid (PMID: 16139832)

Cellular substructure

Cytoplasm (HMDB: HMDB0000767)

Chickpea (FooDB: FOOD00047)

Bean

Pulses (FooDB: FOOD00867)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Purine Degradation (PathBank: SMP0001901)

Role

Industrial application

Pharmaceutical industry

Biomarker

Canavan disease (MarkerDB: MDB00000249)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M-H]-	MetCCS_train_neg	145.233	30932474
[M-H]-	Not Available	148.0	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000107

Predicted Molecular Properties

Property	Value	Source
Water Solubility	63.8 g/L	ALOGPS
logP	-2	ALOGPS
logP	-3.1	ChemAxon
logS	-0.58	ALOGPS
pKa (Strongest Acidic)	8.66	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	128.12 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	52.44 m³·mol⁻¹	ChemAxon
Polarizability	21.79 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	155.246	31661259
DarkChem	[M-H]-	150.649	31661259
AllCCS	[M+H]+	155.338	32859911
AllCCS	[M-H]-	151.601	32859911
DeepCCS	[M+H]+	157.636	30932474
DeepCCS	[M-H]-	155.24	30932474
DeepCCS	[M-2H]-	188.125	30932474
DeepCCS	[M+Na]+	163.548	30932474
AllCCS	[M+H]+	155.3	32859911
AllCCS	[M+H-H2O]+	151.6	32859911
AllCCS	[M+NH4]+	158.8	32859911
AllCCS	[M+Na]+	159.8	32859911
AllCCS	[M-H]-	151.6	32859911
AllCCS	[M+Na-2H]-	151.5	32859911
AllCCS	[M+HCOO]-	151.5	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Pseudouridine	OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)C1=CNC(=O)NC1=O	3282.8	Standard polar	33892256
Pseudouridine	OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)C1=CNC(=O)NC1=O	2232.9	Standard non polar	33892256
Pseudouridine	OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)C1=CNC(=O)NC1=O	2695.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Pseudouridine,1TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](C2=C[NH]C(=O)[NH]C2=O)[C@H](O)[C@@H]1O	2327.9	Semi standard non polar	33892256
Pseudouridine,1TMS,isomer #2	C[Si](C)(C)O[C@H]1[C@H](C2=C[NH]C(=O)[NH]C2=O)O[C@H](CO)[C@H]1O	2333.3	Semi standard non polar	33892256
Pseudouridine,1TMS,isomer #3	C[Si](C)(C)O[C@H]1[C@@H](O)[C@H](C2=C[NH]C(=O)[NH]C2=O)O[C@@H]1CO	2346.0	Semi standard non polar	33892256
Pseudouridine,1TMS,isomer #4	C[Si](C)(C)N1C=C([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)[NH]C1=O	2374.8	Semi standard non polar	33892256
Pseudouridine,1TMS,isomer #5	C[Si](C)(C)N1C(=O)[NH]C=C([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C1=O	2426.1	Semi standard non polar	33892256
Pseudouridine,2TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](C2=C[NH]C(=O)[NH]C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O	2341.0	Semi standard non polar	33892256
Pseudouridine,2TMS,isomer #10	C[Si](C)(C)N1C=C([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)N([Si](C)(C)C)C1=O	2429.6	Semi standard non polar	33892256
Pseudouridine,2TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](C2=C[NH]C(=O)[NH]C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C	2341.3	Semi standard non polar	33892256
Pseudouridine,2TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C)C(=O)[NH]C2=O)[C@H](O)[C@@H]1O	2391.6	Semi standard non polar	33892256
Pseudouridine,2TMS,isomer #4	C[Si](C)(C)OC[C@H]1O[C@@H](C2=C[NH]C(=O)N([Si](C)(C)C)C2=O)[C@H](O)[C@@H]1O	2412.0	Semi standard non polar	33892256
Pseudouridine,2TMS,isomer #5	C[Si](C)(C)O[C@H]1[C@H](C2=C[NH]C(=O)[NH]C2=O)O[C@H](CO)[C@H]1O[Si](C)(C)C	2333.0	Semi standard non polar	33892256
Pseudouridine,2TMS,isomer #6	C[Si](C)(C)O[C@H]1[C@H](C2=CN([Si](C)(C)C)C(=O)[NH]C2=O)O[C@H](CO)[C@H]1O	2393.8	Semi standard non polar	33892256
Pseudouridine,2TMS,isomer #7	C[Si](C)(C)O[C@H]1[C@H](C2=C[NH]C(=O)N([Si](C)(C)C)C2=O)O[C@H](CO)[C@H]1O	2407.2	Semi standard non polar	33892256
Pseudouridine,2TMS,isomer #8	C[Si](C)(C)O[C@H]1[C@@H](O)[C@H](C2=CN([Si](C)(C)C)C(=O)[NH]C2=O)O[C@@H]1CO	2403.5	Semi standard non polar	33892256
Pseudouridine,2TMS,isomer #9	C[Si](C)(C)O[C@H]1[C@@H](O)[C@H](C2=C[NH]C(=O)N([Si](C)(C)C)C2=O)O[C@@H]1CO	2415.5	Semi standard non polar	33892256
Pseudouridine,3TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](C2=C[NH]C(=O)[NH]C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2304.2	Semi standard non polar	33892256
Pseudouridine,3TMS,isomer #10	C[Si](C)(C)O[C@H]1[C@@H](O)[C@H](C2=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C2=O)O[C@@H]1CO	2475.1	Semi standard non polar	33892256
Pseudouridine,3TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C)C(=O)[NH]C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O	2413.0	Semi standard non polar	33892256
Pseudouridine,3TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](C2=C[NH]C(=O)N([Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O	2415.5	Semi standard non polar	33892256
Pseudouridine,3TMS,isomer #4	C[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C)C(=O)[NH]C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C	2406.4	Semi standard non polar	33892256
Pseudouridine,3TMS,isomer #5	C[Si](C)(C)OC[C@H]1O[C@@H](C2=C[NH]C(=O)N([Si](C)(C)C)C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C	2410.4	Semi standard non polar	33892256
Pseudouridine,3TMS,isomer #6	C[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C2=O)[C@H](O)[C@@H]1O	2472.5	Semi standard non polar	33892256
Pseudouridine,3TMS,isomer #7	C[Si](C)(C)O[C@H]1[C@H](C2=CN([Si](C)(C)C)C(=O)[NH]C2=O)O[C@H](CO)[C@H]1O[Si](C)(C)C	2406.6	Semi standard non polar	33892256
Pseudouridine,3TMS,isomer #8	C[Si](C)(C)O[C@H]1[C@H](C2=C[NH]C(=O)N([Si](C)(C)C)C2=O)O[C@H](CO)[C@H]1O[Si](C)(C)C	2410.8	Semi standard non polar	33892256
Pseudouridine,3TMS,isomer #9	C[Si](C)(C)O[C@H]1[C@H](C2=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C2=O)O[C@H](CO)[C@H]1O	2473.0	Semi standard non polar	33892256
Pseudouridine,4TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C)C(=O)[NH]C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2422.1	Semi standard non polar	33892256
Pseudouridine,4TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C)C(=O)[NH]C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2664.9	Standard non polar	33892256
Pseudouridine,4TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C)C(=O)[NH]C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2776.3	Standard polar	33892256
Pseudouridine,4TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](C2=C[NH]C(=O)N([Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2406.3	Semi standard non polar	33892256
Pseudouridine,4TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](C2=C[NH]C(=O)N([Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2630.5	Standard non polar	33892256
Pseudouridine,4TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](C2=C[NH]C(=O)N([Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2620.7	Standard polar	33892256
Pseudouridine,4TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O	2526.8	Semi standard non polar	33892256
Pseudouridine,4TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O	2679.1	Standard non polar	33892256
Pseudouridine,4TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O	2840.6	Standard polar	33892256
Pseudouridine,4TMS,isomer #4	C[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C	2518.3	Semi standard non polar	33892256
Pseudouridine,4TMS,isomer #4	C[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C	2677.4	Standard non polar	33892256
Pseudouridine,4TMS,isomer #4	C[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C	2804.6	Standard polar	33892256
Pseudouridine,4TMS,isomer #5	C[Si](C)(C)O[C@H]1[C@H](C2=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C2=O)O[C@H](CO)[C@H]1O[Si](C)(C)C	2508.8	Semi standard non polar	33892256
Pseudouridine,4TMS,isomer #5	C[Si](C)(C)O[C@H]1[C@H](C2=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C2=O)O[C@H](CO)[C@H]1O[Si](C)(C)C	2650.1	Standard non polar	33892256
Pseudouridine,4TMS,isomer #5	C[Si](C)(C)O[C@H]1[C@H](C2=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C2=O)O[C@H](CO)[C@H]1O[Si](C)(C)C	2772.7	Standard polar	33892256
Pseudouridine,5TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2532.2	Semi standard non polar	33892256
Pseudouridine,5TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2684.7	Standard non polar	33892256
Pseudouridine,5TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2640.2	Standard polar	33892256
Pseudouridine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=C[NH]C(=O)[NH]C2=O)[C@H](O)[C@@H]1O	2584.6	Semi standard non polar	33892256
Pseudouridine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](C2=C[NH]C(=O)[NH]C2=O)O[C@H](CO)[C@H]1O	2588.9	Semi standard non polar	33892256
Pseudouridine,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@H]1[C@@H](O)[C@H](C2=C[NH]C(=O)[NH]C2=O)O[C@@H]1CO	2595.6	Semi standard non polar	33892256
Pseudouridine,1TBDMS,isomer #4	CC(C)(C)[Si](C)(C)N1C=C([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)[NH]C1=O	2682.8	Semi standard non polar	33892256
Pseudouridine,1TBDMS,isomer #5	CC(C)(C)[Si](C)(C)N1C(=O)[NH]C=C([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C1=O	2657.1	Semi standard non polar	33892256
Pseudouridine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=C[NH]C(=O)[NH]C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	2801.9	Semi standard non polar	33892256
Pseudouridine,2TBDMS,isomer #10	CC(C)(C)[Si](C)(C)N1C=C([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2908.3	Semi standard non polar	33892256
Pseudouridine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=C[NH]C(=O)[NH]C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	2794.2	Semi standard non polar	33892256
Pseudouridine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C2=O)[C@H](O)[C@@H]1O	2867.9	Semi standard non polar	33892256
Pseudouridine,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O)[C@@H]1O	2864.8	Semi standard non polar	33892256
Pseudouridine,2TBDMS,isomer #5	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](C2=C[NH]C(=O)[NH]C2=O)O[C@H](CO)[C@H]1O[Si](C)(C)C(C)(C)C	2790.0	Semi standard non polar	33892256
Pseudouridine,2TBDMS,isomer #6	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C2=O)O[C@H](CO)[C@H]1O	2871.0	Semi standard non polar	33892256
Pseudouridine,2TBDMS,isomer #7	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](C2=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C2=O)O[C@H](CO)[C@H]1O	2861.8	Semi standard non polar	33892256
Pseudouridine,2TBDMS,isomer #8	CC(C)(C)[Si](C)(C)O[C@H]1[C@@H](O)[C@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C2=O)O[C@@H]1CO	2875.3	Semi standard non polar	33892256
Pseudouridine,2TBDMS,isomer #9	CC(C)(C)[Si](C)(C)O[C@H]1[C@@H](O)[C@H](C2=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C2=O)O[C@@H]1CO	2869.5	Semi standard non polar	33892256
Pseudouridine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=C[NH]C(=O)[NH]C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	2990.7	Semi standard non polar	33892256
Pseudouridine,3TBDMS,isomer #10	CC(C)(C)[Si](C)(C)O[C@H]1[C@@H](O)[C@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)O[C@@H]1CO	3155.8	Semi standard non polar	33892256
Pseudouridine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	3082.6	Semi standard non polar	33892256
Pseudouridine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	3062.4	Semi standard non polar	33892256
Pseudouridine,3TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	3083.1	Semi standard non polar	33892256
Pseudouridine,3TBDMS,isomer #5	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	3063.7	Semi standard non polar	33892256
Pseudouridine,3TBDMS,isomer #6	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O)[C@@H]1O	3138.7	Semi standard non polar	33892256
Pseudouridine,3TBDMS,isomer #7	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C2=O)O[C@H](CO)[C@H]1O[Si](C)(C)C(C)(C)C	3078.3	Semi standard non polar	33892256
Pseudouridine,3TBDMS,isomer #8	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](C2=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C2=O)O[C@H](CO)[C@H]1O[Si](C)(C)C(C)(C)C	3052.6	Semi standard non polar	33892256
Pseudouridine,3TBDMS,isomer #9	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)O[C@H](CO)[C@H]1O	3144.5	Semi standard non polar	33892256
Pseudouridine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3265.7	Semi standard non polar	33892256
Pseudouridine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3427.5	Standard non polar	33892256
Pseudouridine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3140.9	Standard polar	33892256
Pseudouridine,4TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3237.7	Semi standard non polar	33892256
Pseudouridine,4TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3374.7	Standard non polar	33892256
Pseudouridine,4TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3034.8	Standard polar	33892256
Pseudouridine,4TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	3341.0	Semi standard non polar	33892256
Pseudouridine,4TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	3430.3	Standard non polar	33892256
Pseudouridine,4TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	3153.8	Standard polar	33892256
Pseudouridine,4TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	3337.5	Semi standard non polar	33892256
Pseudouridine,4TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	3430.2	Standard non polar	33892256
Pseudouridine,4TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	3126.3	Standard polar	33892256
Pseudouridine,4TBDMS,isomer #5	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)O[C@H](CO)[C@H]1O[Si](C)(C)C(C)(C)C	3352.2	Semi standard non polar	33892256
Pseudouridine,4TBDMS,isomer #5	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)O[C@H](CO)[C@H]1O[Si](C)(C)C(C)(C)C	3412.3	Standard non polar	33892256
Pseudouridine,4TBDMS,isomer #5	CC(C)(C)[Si](C)(C)O[C@H]1[C@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)O[C@H](CO)[C@H]1O[Si](C)(C)C(C)(C)C	3101.6	Standard polar	33892256
Pseudouridine,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3531.2	Semi standard non polar	33892256
Pseudouridine,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3543.2	Standard non polar	33892256
Pseudouridine,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](C2=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3106.4	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0unc-7930000000-a1e7f343c88a63ac1976	2016-09-22	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (3 TMS) - 70eV, Positive	splash10-0fi0-3494100000-8d726ed412554c1f92f0	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (TMS_1_5) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (TMS_2_5) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (TMS_2_6) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (TMS_2_7) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (TMS_2_8) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (TMS_2_9) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (TMS_2_10) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (TMS_3_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (TMS_3_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (TMS_3_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (TMS_3_5) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (TMS_3_6) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pseudouridine GC-MS (TMS_3_7) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pseudouridine LC-ESI-IT , negative-QTOF	splash10-0udi-0900000000-6ade42aaa885371e176c	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pseudouridine LC-ESI-QTOF 10V, positive-QTOF	splash10-0a4i-0190000000-129f123affa0ecbf7a59	2020-07-21	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pseudouridine LC-ESI-QTOF 20V, positive-QTOF	splash10-052f-0910000000-302fbdef606070bd5a67	2020-07-21	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pseudouridine LC-ESI-QTOF 40V, positive-QTOF	splash10-001i-9300000000-11f5761be16d1b061df5	2020-07-21	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pseudouridine 30V, Negative-QTOF	splash10-0006-9600000000-7585746143c62ab3f832	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pseudouridine 40V, Negative-QTOF	splash10-0006-9100000000-010da2c57a936868eecc	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pseudouridine 40V, Positive-QTOF	splash10-0kai-9200000000-12f986238bdf05dc39b9	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pseudouridine 30V, Positive-QTOF	splash10-001i-9400000000-b6dbdfa2d4643fc13e70	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pseudouridine 10V, Positive-QTOF	splash10-0a4i-0190000000-129f123affa0ecbf7a59	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pseudouridine 20V, Positive-QTOF	splash10-052f-0910000000-302fbdef606070bd5a67	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pseudouridine 0V, Positive-QTOF	splash10-0bta-0890000000-2b3810ae2bbe68268b17	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pseudouridine 40V, Positive-QTOF	splash10-001i-9300000000-7e64dc8404ac65411358	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pseudouridine 0V, Positive-QTOF	splash10-052b-0290000000-7cf7d5be6f7a84299cab	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pseudouridine 10V, Positive-QTOF	splash10-0a4i-0950000000-de2a45f204636756b9c4	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pseudouridine 30V, Positive-QTOF	splash10-00l6-9000000000-b4060d47530bdf70d6cc	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pseudouridine 10V, Positive-QTOF	splash10-0a4i-3920000000-15bb158a77906d0f87b5	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pseudouridine 20V, Negative-QTOF	splash10-0udi-2900000000-600643d24abd3ba9b5f1	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pseudouridine 10V, Negative-QTOF	splash10-0udi-0920000000-a73049fd7001db7f72d5	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pseudouridine 20V, Negative-QTOF	splash10-0udi-0900000000-46e1b064445ad43a60fd	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pseudouridine 10V, Positive-QTOF	splash10-0002-0490000000-226d044c24dd80a7c2ca	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pseudouridine 20V, Positive-QTOF	splash10-0h0s-2980000000-add34ee37b95c102114d	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pseudouridine 40V, Positive-QTOF	splash10-06rm-5900000000-8d66d80928e84e9c93fd	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pseudouridine 10V, Negative-QTOF	splash10-0006-9360000000-3bd8fcdd66c5d245778e	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pseudouridine 20V, Negative-QTOF	splash10-0006-9210000000-f551740a13c90ff1d324	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pseudouridine 40V, Negative-QTOF	splash10-0006-9000000000-bf4e4234a47d8aa03828	2015-09-15	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Experimental 1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	2012-12-04	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm (predicted from logP)

Biospecimen Locations

Amniotic Fluid
Blood
Feces
Urine

Tissue Locations

Placenta

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Amniotic Fluid	Detected and Quantified	1.29 +/- 1.07 uM	Adult (>18 years old)	Female	Normal	16139832	details
Blood	Detected and Quantified	2.0492 +/- 23.770 uM	Children (3 months - 6 years old)	Not Specified	Normal	12675874	details
Blood	Detected and Quantified	3.18 +/- 0.99 uM	Adult (>18 years old)	Both	Normal	16139832	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	29808030	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	27543620	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	25037050	details
Urine	Detected and Quantified	63.47 +/- 32.76 umol/mmol creatinine	Infant (0-1 year old)	Both	Normal	2026685	details
Urine	Detected and Quantified	29.8 (21.8-47.3) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	24023812	details
Urine	Detected and Quantified	12.5 (6.5-20.4) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	Geigy Scientific ...	details
Urine	Detected and Quantified	26.02 +/- 4.62 umol/mmol creatinine	Adult (>18 years old)	Female	Normal	9129323	details
Urine	Detected and Quantified	25.0 +/- 5.0 umol/mmol creatinine	Adult (>18 years old)	Male	Normal	9129323	details
Urine	Detected and Quantified	25.5 +/- 4.8 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	9129323	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	21389975	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	24023812	details
Urine	Detected and Quantified	13.467 (8.307-18.627) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	15116424	details
Urine	Detected and Quantified	28.9 (13.3-41.3) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	24023812	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	53.689 +/- 87.705 uM	Children (3 months - 6 years old)	Not Specified	Uremia	12675874	details
Blood	Detected and Quantified	16.70 +/- 3.72 uM	Adult (>18 years old)	Both	Canavan disease	16139832	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal cancer	25037050	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal Cancer	27015276	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal Cancer	27275383	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Female	Epithelial ovarian cancer	23163809	details

Associated Disorders and Diseases

Disease References

Canavan disease
Tavazzi B, Lazzarino G, Leone P, Amorini AM, Bellia F, Janson CG, Di Pietro V, Ceccarelli L, Donzelli S, Francis JS, Giardina B: Simultaneous high performance liquid chromatographic separation of purines, pyrimidines, N-acetylated amino acids, and dicarboxylic acids for the chemical diagnosis of inborn errors of metabolism. Clin Biochem. 2005 Nov;38(11):997-1008. Epub 2005 Sep 1. [PubMed:16139832 ]
Uremia
Vanholder R, De Smet R, Glorieux G, Argiles A, Baurmeister U, Brunet P, Clark W, Cohen G, De Deyn PP, Deppisch R, Descamps-Latscha B, Henle T, Jorres A, Lemke HD, Massy ZA, Passlick-Deetjen J, Rodriguez M, Stegmayr B, Stenvinkel P, Tetta C, Wanner C, Zidek W: Review on uremic toxins: classification, concentration, and interindividual variability. Kidney Int. 2003 May;63(5):1934-43. doi: 10.1046/j.1523-1755.2003.00924.x. [PubMed:12675874 ]
Colorectal cancer
Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ] Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ] Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]

Associated OMIM IDs

271900 (Canavan disease)
114500 (Colorectal cancer)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Pseudouridine

METLIN ID

5734

PubChem Compound

15047

PDB ID

Not Available

ChEBI ID

17802

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

MDB00000249

Good Scents ID

Not Available

References

Synthesis Reference

anessian, Stephen; Machaalani, Roger. A highly stereo-controlled and efficient synthesis of a- and b-pseudouridines. Tetrahedron Letters (2003), 44(45), 8321-8323.

Material Safety Data Sheet (MSDS)

Not Available

General References

Lee SH, Jung BH, Kim SY, Chung BC: A rapid and sensitive method for quantitation of nucleosides in human urine using liquid chromatography/mass spectrometry with direct urine injection. Rapid Commun Mass Spectrom. 2004;18(9):973-7. [PubMed:15116424 ]
Shoemaker JD, Elliott WH: Automated screening of urine samples for carbohydrates, organic and amino acids after treatment with urease. J Chromatogr. 1991 Jan 2;562(1-2):125-38. [PubMed:2026685 ]
Uziel M, Smith LH, Taylor SA: Modified nucleosides in urine: selective removal and analysis. Clin Chem. 1976 Sep;22(9):1451-5. [PubMed:954194 ]
Bernert JT Jr, Bell CJ, Guntupalli J, Hannon WH: Pseudouridine is unsuitable as an endogenous renal clearance marker. Clin Chem. 1988 Jun;34(6):1011-7. [PubMed:3378317 ]
Woodcock TM, Chou TC, Tan CT, Sternberg SS, Philips FS, Young CW, Burchenal JH: Biochemical, pharmacological, and phase I clinical evaluation of pseudoisocytidine. Cancer Res. 1980 Nov;40(11):4243-9. [PubMed:7471064 ]
Colonna A, Russo T, Esposito F, Salvatore F, Cimino F: Determination of pseudouridine and other nucleosides in human blood serum by high-performance liquid chromatography. Anal Biochem. 1983 Apr 1;130(1):19-26. [PubMed:6869800 ]
Mak TW, Ho SS, Ho CS, Jones MG, Lai CK, Lam CW: Pleural fluid pseudouridine in malignant and benign pleural effusions. Ann Clin Biochem. 1998 Jan;35 ( Pt 1):94-8. [PubMed:9463745 ]
Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]
Hamma T, Ferre-D'Amare AR: Pseudouridine synthases. Chem Biol. 2006 Nov;13(11):1125-35. doi: 10.1016/j.chembiol.2006.09.009. [PubMed:17113994 ]

Only showing the first 10 proteins. There are 14 proteins in total.

Show all enzymes and transporters

Enzymes

Enzyme Details

1. tRNA pseudouridine synthase A, mitochondrial

General function:: Involved in RNA binding
Specific function:: Converts specific uridines to PSI in a number of tRNA substrates. Acts on positions 27/28 in the anticodon stem and also positions 34 and 36 in the anticodon of an intron containing tRNA. Involved in regulation of nuclear receptor activity possibly through pseudouridylation of SRA1 RNA
Gene Name:: PUS1
Uniprot ID:: Q9Y606
Molecular weight:: 47469.7

Enzyme Details

2. H/ACA ribonucleoprotein complex subunit 4

General function:: Involved in RNA processing
Specific function:: Required for ribosome biogenesis and telomere maintenance. Probable catalytic subunit of H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex, which catalyzes pseudouridylation of rRNA. This involves the isomerization of uridine such that the ribose is subsequently attached to C5, instead of the normal N1. Each rRNA can contain up to 100 pseudouridine ('psi') residues, which may serve to stabilize the conformation of rRNAs. Also required for correct processing or intranuclear trafficking of TERC, the RNA component of the telomerase reverse transcriptase (TERT) holoenzyme
Gene Name:: DKC1
Uniprot ID:: O60832
Molecular weight:: 57673.7

Enzyme Details

3. Putative tRNA pseudouridine synthase Pus10

General function:: Involved in RNA binding
Specific function:: Pseudouridylate synthases catalyze pseudouridination of structural RNAs, including transfer, ribosomal, and splicing RNAs. PUS10 catalyzes the formation of the universal psi55 in the GC loop of transfer RNAs (Probable). Modulator of TRAIL-induced cell death via activation of procaspase 8 and BID cleavage. Required for the progression of the apoptotic signal through intrinsic mitochondrial cell death
Gene Name:: PUS10
Uniprot ID:: Q3MIT2
Molecular weight:: 60243.7

Enzyme Details

4. tRNA pseudouridine synthase 3

General function:: Involved in RNA binding
Specific function:: Formation of pseudouridine at position 39 in the anticodon stem and loop of transfer RNAs
Gene Name:: PUS3
Uniprot ID:: Q9BZE2
Molecular weight:: 55647.0

Enzyme Details

5. Pseudouridylate synthase 7 homolog