Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (4) Show 4 proteins XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2006-10-17 09:25:06 UTC

Update Date

2022-03-07 02:49:25 UTC

HMDB ID

HMDB0005026

Secondary Accession Numbers

HMDB05026

Metabolite Identification

Common Name

Rabeprazole

Description

Rabeprazole, also known as clofezone or eraloc, belongs to the class of organic compounds known as sulfinylbenzimidazoles. These are polycyclic aromatic compounds containing a sulfinyl group attached at the position 2 of a benzimidazole moiety. Rabeprazole is a drug which is used for the treatment of acid-reflux disorders (gerd), peptic ulcer disease, h. pylori eradication, and prevention of gastroinetestinal bleeds with nsaid use. In humans, rabeprazole is involved in the rabeprazole metabolism pathway. Rabeprazole is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on Rabeprazole.

Structure

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

HMDB0005026
     RDKit          3D
Rabeprazole
 46 48  0  0  0  0  0  0  0  0999 V2000
    7.0669   -2.0751    0.1686 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7278   -2.0129    0.4915 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3086   -0.7898    0.9264 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4964    0.3198   -0.0816 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7458    0.0456   -1.3490 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4098   -0.0784   -1.1425 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4006    0.6969   -0.7110 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5834    2.0051   -0.3537 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4703    2.7357    0.0823 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2500    2.1623    0.1469 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0503    0.8829   -0.1992 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2929    0.3040   -0.1128 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4722    1.5300    0.4847 S   0  0  0  0  0  4  0  0  0  0  0  0
   -2.5354    2.7354   -0.4339 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0903    0.7709    0.5703 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6369    0.1210    1.6140 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8687   -0.3183    1.3219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8514   -1.0249    2.0072 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0657   -1.3487    1.4373 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2925   -0.9459    0.1361 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3356   -0.2426   -0.5705 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1168    0.0743    0.0223 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0192    0.7314   -0.4023 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1145    0.1409   -0.6288 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9393   -1.2506   -1.0133 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3379   -1.3802   -0.6437 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6415   -1.7956    1.0956 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3507   -3.1218   -0.0822 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2287   -0.8647    1.1806 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8581   -0.4562    1.8522 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5844    0.4456   -0.2875 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1884    1.2485    0.4173 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1869   -0.8585   -1.8604 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8984    0.9183   -2.0619 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5043    2.5570   -0.3822 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5484    3.7733    0.3793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6364   -0.1666   -1.0544 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3126   -0.5280    0.6498 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6556   -1.3277    3.0146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8330   -1.9036    1.9806 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2617   -1.2080   -0.3094 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5571    0.0483   -1.5768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9108    1.1495   -1.3553 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0095   -1.3139   -2.1385 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0377   -1.7348   -0.6453 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8061   -1.8315   -0.5831 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 11 24  2  0
 24 25  1  0
 24  7  1  0
 23 15  1  0
 22 17  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  3 29  1  0
  3 30  1  0
  4 31  1  0
  4 32  1  0
  5 33  1  0
  5 34  1  0
  8 35  1  0
  9 36  1  0
 12 37  1  0
 12 38  1  0
 18 39  1  0
 19 40  1  0
 20 41  1  0
 21 42  1  0
 23 43  1  0
 25 44  1  0
 25 45  1  0
 25 46  1  0
M  END

1129
  Mrv0541 02231215162D          

 25 27  0  0  1  0            999 V2000
    5.1662    1.2111    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    8.0537   -0.9323    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.5288   -2.3613    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5787    1.9257    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8597    1.8751    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8597    0.5472    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.8162    1.2111    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.5787    0.4967    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4037    0.4967    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8162   -0.2178    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6412   -0.2178    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3412    1.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    1.6236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8788   -0.9323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2913   -1.6468    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    0.7986    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4037   -0.9323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0537    0.4967    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1163   -1.6468    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    2.0361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6412    1.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    0.3861    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    1.6236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.7986    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3538   -2.3613    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  2  0  0  0  0
  1  8  1  0  0  0  0
  1 12  1  0  0  0  0
  2 11  1  0  0  0  0
  2 14  1  0  0  0  0
  3 19  1  0  0  0  0
  3 25  1  0  0  0  0
  5 12  1  0  0  0  0
  5 13  1  0  0  0  0
  6 12  2  0  0  0  0
  6 16  1  0  0  0  0
  7  9  2  0  0  0  0
  7 21  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 17  1  0  0  0  0
 11 18  1  0  0  0  0
 13 16  1  0  0  0  0
 13 20  2  0  0  0  0
 14 15  1  0  0  0  0
 15 19  1  0  0  0  0
 16 22  2  0  0  0  0
 18 21  2  0  0  0  0
 20 23  1  0  0  0  0
 22 24  1  0  0  0  0
 23 24  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0005026

> <DATABASE_NAME>
hmdb

> <SMILES>
COCCCOC1=C(C)C(CS(=O)C2=NC3=CC=CC=C3N2)=NC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C18H21N3O3S/c1-13-16(19-9-8-17(13)24-11-5-10-23-2)12-25(22)18-20-14-6-3-4-7-15(14)21-18/h3-4,6-9H,5,10-12H2,1-2H3,(H,20,21)

> <INCHI_KEY>
YREYEVIYCVEVJK-UHFFFAOYSA-N

> <FORMULA>
C18H21N3O3S

> <MOLECULAR_WEIGHT>
359.443

> <EXACT_MASS>
359.130362243

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
39.63690033611189

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-{[4-(3-methoxypropoxy)-3-methylpyridin-2-yl]methanesulfinyl}-1H-1,3-benzodiazole

> <ALOGPS_LOGP>
2.04

> <JCHEM_LOGP>
2.0907432303333326

> <ALOGPS_LOGS>
-3.03

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
17.329381007589777

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.346710821346507

> <JCHEM_PKA_STRONGEST_BASIC>
4.23997374588058

> <JCHEM_POLAR_SURFACE_AREA>
77.10000000000001

> <JCHEM_REFRACTIVITY>
98.0668

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.36e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
rabeprazole

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0005026
     RDKit          3D
Rabeprazole
 46 48  0  0  0  0  0  0  0  0999 V2000
    7.0669   -2.0751    0.1686 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7278   -2.0129    0.4915 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3086   -0.7898    0.9264 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4964    0.3198   -0.0816 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7458    0.0456   -1.3490 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4098   -0.0784   -1.1425 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4006    0.6969   -0.7110 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5834    2.0051   -0.3537 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4703    2.7357    0.0823 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2500    2.1623    0.1469 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0503    0.8829   -0.1992 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2929    0.3040   -0.1128 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4722    1.5300    0.4847 S   0  0  0  0  0  4  0  0  0  0  0  0
   -2.5354    2.7354   -0.4339 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0903    0.7709    0.5703 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6369    0.1210    1.6140 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8687   -0.3183    1.3219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8514   -1.0249    2.0072 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0657   -1.3487    1.4373 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2925   -0.9459    0.1361 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3356   -0.2426   -0.5705 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1168    0.0743    0.0223 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0192    0.7314   -0.4023 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1145    0.1409   -0.6288 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9393   -1.2506   -1.0133 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3379   -1.3802   -0.6437 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6415   -1.7956    1.0956 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3507   -3.1218   -0.0822 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2287   -0.8647    1.1806 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8581   -0.4562    1.8522 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5844    0.4456   -0.2875 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1884    1.2485    0.4173 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1869   -0.8585   -1.8604 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8984    0.9183   -2.0619 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5043    2.5570   -0.3822 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5484    3.7733    0.3793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6364   -0.1666   -1.0544 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3126   -0.5280    0.6498 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6556   -1.3277    3.0146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8330   -1.9036    1.9806 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2617   -1.2080   -0.3094 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5571    0.0483   -1.5768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9108    1.1495   -1.3553 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0095   -1.3139   -2.1385 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0377   -1.7348   -0.6453 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8061   -1.8315   -0.5831 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 11 24  2  0
 24 25  1  0
 24  7  1  0
 23 15  1  0
 22 17  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  3 29  1  0
  3 30  1  0
  4 31  1  0
  4 32  1  0
  5 33  1  0
  5 34  1  0
  8 35  1  0
  9 36  1  0
 12 37  1  0
 12 38  1  0
 18 39  1  0
 19 40  1  0
 20 41  1  0
 21 42  1  0
 23 43  1  0
 25 44  1  0
 25 45  1  0
 25 46  1  0
M  END

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 1129                                              
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  S   UNK     0       9.644   2.261   0.000  0.00  0.00           S+0
HETATM    2  O   UNK     0      15.034  -1.740   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      19.654  -4.408   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      10.414   3.595   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       7.205   3.500   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0       7.205   1.021   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0      12.724   2.261   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      10.414   0.927   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.954   0.927   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      12.724  -0.407   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      14.264  -0.407   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.104   2.261   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.748   3.031   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      16.574  -1.740   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      17.344  -3.074   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.748   1.491   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      11.954  -1.740   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      15.034   0.927   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      18.884  -3.074   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.414   3.801   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      14.264   2.261   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.414   0.721   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.080   3.031   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.080   1.491   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      21.194  -4.408   0.000  0.00  0.00           C+0
CONECT    1    4    8   12                                                  
CONECT    2   11   14                                                       
CONECT    3   19   25                                                       
CONECT    4    1                                                            
CONECT    5   12   13                                                       
CONECT    6   12   16                                                       
CONECT    7    9   21                                                       
CONECT    8    1    9                                                       
CONECT    9    7    8   10                                                  
CONECT   10    9   11   17                                                  
CONECT   11    2   10   18                                                  
CONECT   12    1    5    6                                                  
CONECT   13    5   16   20                                                  
CONECT   14    2   15                                                       
CONECT   15   14   19                                                       
CONECT   16    6   13   22                                                  
CONECT   17   10                                                            
CONECT   18   11   21                                                       
CONECT   19    3   15                                                       
CONECT   20   13   23                                                       
CONECT   21    7   18                                                       
CONECT   22   16   24                                                       
CONECT   23   20   24                                                       
CONECT   24   22   23                                                       
CONECT   25    3                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   54    0
END

COMPND    HMDB0251094
HETATM    1  C1  UNL     1      -3.156  -2.217  -0.347  1.00  0.00           C  
HETATM    2  O1  UNL     1      -3.139  -0.941   0.211  1.00  0.00           O  
HETATM    3  C2  UNL     1      -4.246  -0.727   1.027  1.00  0.00           C  
HETATM    4  C3  UNL     1      -4.215   0.664   1.627  1.00  0.00           C  
HETATM    5  C4  UNL     1      -4.222   1.727   0.555  1.00  0.00           C  
HETATM    6  O2  UNL     1      -3.150   1.607  -0.268  1.00  0.00           O  
HETATM    7  C5  UNL     1      -1.801   1.692  -0.122  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.118   1.972   1.041  1.00  0.00           C  
HETATM    9  C7  UNL     1       0.274   2.025   1.022  1.00  0.00           C  
HETATM   10  N1  UNL     1       0.980   1.808  -0.116  1.00  0.00           N  
HETATM   11  C8  UNL     1       0.345   1.533  -1.268  1.00  0.00           C  
HETATM   12  C9  UNL     1       1.120   1.297  -2.511  1.00  0.00           C  
HETATM   13  S1  UNL     1       2.888   1.436  -2.207  1.00  0.00           S  
HETATM   14  O3  UNL     1       3.685   1.368  -3.483  1.00  0.00           O  
HETATM   15  C10 UNL     1       3.440   0.274  -1.018  1.00  0.00           C  
HETATM   16  N2  UNL     1       3.477   0.520   0.312  1.00  0.00           N  
HETATM   17  C11 UNL     1       3.940  -0.539   0.972  1.00  0.00           C  
HETATM   18  C12 UNL     1       4.150  -0.751   2.313  1.00  0.00           C  
HETATM   19  C13 UNL     1       4.647  -1.968   2.723  1.00  0.00           C  
HETATM   20  C14 UNL     1       4.933  -2.967   1.802  1.00  0.00           C  
HETATM   21  C15 UNL     1       4.707  -2.707   0.481  1.00  0.00           C  
HETATM   22  C16 UNL     1       4.211  -1.507   0.016  1.00  0.00           C  
HETATM   23  N3  UNL     1       3.896  -0.981  -1.182  1.00  0.00           N  
HETATM   24  C17 UNL     1      -1.020   1.478  -1.264  1.00  0.00           C  
HETATM   25  C18 UNL     1      -1.702   1.177  -2.527  1.00  0.00           C  
HETATM   26  H1  UNL     1      -2.284  -2.402  -0.997  1.00  0.00           H  
HETATM   27  H2  UNL     1      -4.062  -2.367  -0.984  1.00  0.00           H  
HETATM   28  H3  UNL     1      -3.194  -2.965   0.457  1.00  0.00           H  
HETATM   29  H4  UNL     1      -5.188  -0.943   0.514  1.00  0.00           H  
HETATM   30  H5  UNL     1      -4.155  -1.453   1.868  1.00  0.00           H  
HETATM   31  H6  UNL     1      -3.428   0.772   2.381  1.00  0.00           H  
HETATM   32  H7  UNL     1      -5.181   0.800   2.193  1.00  0.00           H  
HETATM   33  H8  UNL     1      -4.343   2.741   1.009  1.00  0.00           H  
HETATM   34  H9  UNL     1      -5.165   1.529  -0.045  1.00  0.00           H  
HETATM   35  H10 UNL     1      -1.665   2.160   1.949  1.00  0.00           H  
HETATM   36  H11 UNL     1       0.788   2.247   1.955  1.00  0.00           H  
HETATM   37  H12 UNL     1       0.818   1.986  -3.300  1.00  0.00           H  
HETATM   38  H13 UNL     1       0.872   0.245  -2.829  1.00  0.00           H  
HETATM   39  H14 UNL     1       3.945  -0.010   3.073  1.00  0.00           H  
HETATM   40  H15 UNL     1       4.815  -2.137   3.792  1.00  0.00           H  
HETATM   41  H16 UNL     1       5.327  -3.920   2.172  1.00  0.00           H  
HETATM   42  H17 UNL     1       4.923  -3.473  -0.249  1.00  0.00           H  
HETATM   43  H18 UNL     1       3.988  -1.462  -2.091  1.00  0.00           H  
HETATM   44  H19 UNL     1      -1.689   2.094  -3.166  1.00  0.00           H  
HETATM   45  H20 UNL     1      -2.794   0.938  -2.389  1.00  0.00           H  
HETATM   46  H21 UNL     1      -1.254   0.347  -3.099  1.00  0.00           H  
CONECT    1    2   26   27   28
CONECT    2    3
CONECT    3    4   29   30
CONECT    4    5   31   32
CONECT    5    6   33   34
CONECT    6    7
CONECT    7    8    8   24
CONECT    8    9   35
CONECT    9   10   10   36
CONECT   10   11
CONECT   11   12   24   24
CONECT   12   13   37   38
CONECT   13   14   14   15
CONECT   15   16   16   23
CONECT   16   17
CONECT   17   18   18   22
CONECT   18   19   39
CONECT   19   20   20   40
CONECT   20   21   41
CONECT   21   22   22   42
CONECT   22   23
CONECT   23   43
CONECT   24   25
CONECT   25   44   45   46
END

HMDB0005026
     RDKit          3D
Rabeprazole
 46 48  0  0  0  0  0  0  0  0999 V2000
    7.0669   -2.0751    0.1686 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7278   -2.0129    0.4915 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3086   -0.7898    0.9264 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4964    0.3198   -0.0816 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7458    0.0456   -1.3490 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4098   -0.0784   -1.1425 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4006    0.6969   -0.7110 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5834    2.0051   -0.3537 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4703    2.7357    0.0823 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2500    2.1623    0.1469 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0503    0.8829   -0.1992 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2929    0.3040   -0.1128 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4722    1.5300    0.4847 S   0  0  0  0  0  4  0  0  0  0  0  0
   -2.5354    2.7354   -0.4339 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0903    0.7709    0.5703 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6369    0.1210    1.6140 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8687   -0.3183    1.3219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8514   -1.0249    2.0072 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0657   -1.3487    1.4373 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2925   -0.9459    0.1361 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3356   -0.2426   -0.5705 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1168    0.0743    0.0223 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0192    0.7314   -0.4023 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1145    0.1409   -0.6288 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9393   -1.2506   -1.0133 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3379   -1.3802   -0.6437 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6415   -1.7956    1.0956 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3507   -3.1218   -0.0822 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2287   -0.8647    1.1806 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8581   -0.4562    1.8522 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5844    0.4456   -0.2875 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1884    1.2485    0.4173 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1869   -0.8585   -1.8604 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8984    0.9183   -2.0619 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5043    2.5570   -0.3822 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5484    3.7733    0.3793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6364   -0.1666   -1.0544 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3126   -0.5280    0.6498 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6556   -1.3277    3.0146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8330   -1.9036    1.9806 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2617   -1.2080   -0.3094 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5571    0.0483   -1.5768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9108    1.1495   -1.3553 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0095   -1.3139   -2.1385 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0377   -1.7348   -0.6453 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8061   -1.8315   -0.5831 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 11 24  2  0
 24 25  1  0
 24  7  1  0
 23 15  1  0
 22 17  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  3 29  1  0
  3 30  1  0
  4 31  1  0
  4 32  1  0
  5 33  1  0
  5 34  1  0
  8 35  1  0
  9 36  1  0
 12 37  1  0
 12 38  1  0
 18 39  1  0
 19 40  1  0
 20 41  1  0
 21 42  1  0
 23 43  1  0
 25 44  1  0
 25 45  1  0
 25 46  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Clofezone	ChEBI
Eraloc	Kegg
Aciphex	HMDB, MeSH
Habeprazole	HMDB
Pariet	HMDB, MeSH
Pariets	HMDB
Rabeprazole sodium	HMDB, MeSH
Sodium rabeprazole	HMDB
Dexrabeprazole	MeSH, HMDB
1H-Benzimidazole, 2-(((4-(3-methoxypropoxy)-3-methyl-2-pyridinyl)methyl)sulfinyl)-, sodium salt	MeSH, HMDB
2-((4-(3-Methoxypropoxy)-3-methylpyridin-2-yl)methylsulfinyl)-1H-benzimidazole	MeSH, HMDB
Sodium, rabeprazole	MeSH, HMDB

Chemical Formula

C₁₈H₂₁N₃O₃S

Average Molecular Weight

359.443

Monoisotopic Molecular Weight

359.130362243

IUPAC Name

2-{[4-(3-methoxypropoxy)-3-methylpyridin-2-yl]methanesulfinyl}-1H-1,3-benzodiazole

Traditional Name

rabeprazole

CAS Registry Number

117976-89-3

SMILES

COCCCOC1=C(C)C(CS(=O)C2=NC3=CC=CC=C3N2)=NC=C1

InChI Identifier

InChI=1S/C18H21N3O3S/c1-13-16(19-9-8-17(13)24-11-5-10-23-2)12-25(22)18-20-14-6-3-4-7-15(14)21-18/h3-4,6-9H,5,10-12H2,1-2H3,(H,20,21)

InChI Key

YREYEVIYCVEVJK-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sulfinylbenzimidazoles. These are polycyclic aromatic compounds containing a sulfinyl group attached at the position 2 of a benzimidazole moiety.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzimidazoles

Sub Class

Sulfinylbenzimidazoles

Direct Parent

Sulfinylbenzimidazoles

Alternative Parents

Substituents

Sulfinylbenzimidazole
Alkyl aryl ether
Methylpyridine
Pyridine
Benzenoid
Azole
Imidazole
Heteroaromatic compound
Sulfoxide
Sulfinyl compound
Ether
Dialkyl ether
Azacycle
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

sulfoxide (CHEBI:8768 )
pyridines (CHEBI:8768 )
benzimidazoles (CHEBI:8768 )

Ontology

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	101.7 - 103.9 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.34 g/L	ALOGPS
logP	2.04	ALOGPS
logP	2.09	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	9.35	ChemAxon
pKa (Strongest Basic)	4.24	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	77.1 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	98.07 m³·mol⁻¹	ChemAxon
Polarizability	39.64 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	182.045	31661259
DarkChem	[M-H]-	183.37	31661259
DeepCCS	[M+H]+	192.369	30932474
DeepCCS	[M-H]-	189.869	30932474
DeepCCS	[M-2H]-	224.488	30932474
DeepCCS	[M+Na]+	200.778	30932474
AllCCS	[M+H]+	184.9	32859911
AllCCS	[M+H-H2O]+	182.1	32859911
AllCCS	[M+NH4]+	187.5	32859911
AllCCS	[M+Na]+	188.3	32859911
AllCCS	[M-H]-	184.1	32859911
AllCCS	[M+Na-2H]-	184.1	32859911
AllCCS	[M+HCOO]-	184.3	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Rabeprazole	COCCCOC1=C(C)C(CS(=O)C2=NC3=CC=CC=C3N2)=NC=C1	4061.7	Standard polar	33892256
Rabeprazole	COCCCOC1=C(C)C(CS(=O)C2=NC3=CC=CC=C3N2)=NC=C1	3018.8	Standard non polar	33892256
Rabeprazole	COCCCOC1=C(C)C(CS(=O)C2=NC3=CC=CC=C3N2)=NC=C1	3268.7	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Rabeprazole,1TMS,isomer #1	COCCCOC1=CC=NC(CS(=O)C2=NC3=CC=CC=C3N2[Si](C)(C)C)=C1C	3079.2	Semi standard non polar	33892256
Rabeprazole,1TMS,isomer #1	COCCCOC1=CC=NC(CS(=O)C2=NC3=CC=CC=C3N2[Si](C)(C)C)=C1C	2996.9	Standard non polar	33892256
Rabeprazole,1TMS,isomer #1	COCCCOC1=CC=NC(CS(=O)C2=NC3=CC=CC=C3N2[Si](C)(C)C)=C1C	3880.2	Standard polar	33892256
Rabeprazole,1TBDMS,isomer #1	COCCCOC1=CC=NC(CS(=O)C2=NC3=CC=CC=C3N2[Si](C)(C)C(C)(C)C)=C1C	3219.6	Semi standard non polar	33892256
Rabeprazole,1TBDMS,isomer #1	COCCCOC1=CC=NC(CS(=O)C2=NC3=CC=CC=C3N2[Si](C)(C)C(C)(C)C)=C1C	3206.9	Standard non polar	33892256
Rabeprazole,1TBDMS,isomer #1	COCCCOC1=CC=NC(CS(=O)C2=NC3=CC=CC=C3N2[Si](C)(C)C(C)(C)C)=C1C	3908.5	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Rabeprazole GC-MS (Non-derivatized) - 70eV, Positive	splash10-009e-9843000000-7b2764dc90023b55c85c	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Rabeprazole GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Rabeprazole GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rabeprazole 10V, Positive-QTOF	splash10-03dl-2159000000-f97510bdc8045ab08ca6	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rabeprazole 20V, Positive-QTOF	splash10-006x-5792000000-af268bb77b35247f0f41	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rabeprazole 40V, Positive-QTOF	splash10-00dl-9800000000-6bea6647768de1869c4d	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rabeprazole 10V, Negative-QTOF	splash10-066r-1938000000-25678fb8a17be5befc29	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rabeprazole 20V, Negative-QTOF	splash10-014i-0900000000-c503bc067607aca1451e	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rabeprazole 40V, Negative-QTOF	splash10-014i-2910000000-aa7552fe843abc4a67e6	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rabeprazole 10V, Negative-QTOF	splash10-0a4i-0119000000-c5f221b3ffcf7b5cc55c	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rabeprazole 20V, Negative-QTOF	splash10-014i-0900000000-3214248b0f4d9b60f153	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rabeprazole 40V, Negative-QTOF	splash10-014i-0900000000-9c4b8759dd61ba097216	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rabeprazole 10V, Positive-QTOF	splash10-03di-0093000000-14b0419adbad3c76149e	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rabeprazole 20V, Positive-QTOF	splash10-0229-1950000000-ce8b99f657880db6f1d0	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rabeprazole 40V, Positive-QTOF	splash10-08ml-2910000000-2fbee5190b8417e0ac8a	2021-09-22	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Membrane (predicted from logP)

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Name	SMPDB/PathBank	KEGG
Rabeprazole Action Pathway		Not Available
Rabeprazole Metabolism Pathway		Not Available

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB01129

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023595

KNApSAcK ID

Not Available

Chemspider ID

4853

KEGG Compound ID

C07864

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Rabeprazole

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

8768

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Souda, Shigeru; Ueda, Norihiro; Miyazawa, Shuhei; Tagami, Katsuya; Nomoto, Seiichiro; Okita, Makoto; Shimomura, Naoyuki; Kaneko, Toshihiko; Fujimoto, Masatoshi; et al. Preparation of 2-[(4-alkoxypyrid-2-yl)methylthio]benzimidazoles, -benzothiazoles, and -benzoxazoles as ulcer inhibitors. Eur. Pat. Appl. (1988), 96 pp. CODEN: EPXXDW EP 268956 A2 19880601 CAN 110:23889 AN 1989:23889

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Enzymes

Enzyme Details

1. Cytochrome P450 3A4

General function:: Involved in monooxygenase activity
Specific function:: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It performs a variety of oxidation reactions (e.g. caffeine 8-oxidation, omeprazole sulphoxidation, midazolam 1'-hydroxylation and midazolam 4-hydroxylation) of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,8-cineole 2-exo-monooxygenase. The enzyme also hydroxylates etoposide.
Gene Name:: CYP3A4
Uniprot ID:: P08684
Molecular weight:: 57255.585

Enzyme Details

2. Cytochrome P450 2C19

General function:: Involved in monooxygenase activity
Specific function:: Responsible for the metabolism of a number of therapeutic agents such as the anticonvulsant drug S-mephenytoin, omeprazole, proguanil, certain barbiturates, diazepam, propranolol, citalopram and imipramine.
Gene Name:: CYP2C19
Uniprot ID:: P33261
Molecular weight:: 55944.565

Enzyme Details

3. Potassium-transporting ATPase subunit beta

General function:: Involved in sodium:potassium-exchanging ATPase activity
Specific function:: Not Available
Gene Name:: ATP4B
Uniprot ID:: P51164
Molecular weight:: 33367.0

Enzyme Details

4. Potassium-transporting ATPase alpha chain 1

General function:: Involved in ATP binding
Specific function:: Catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. Responsible for acid production in the stomach.
Gene Name:: ATP4A
Uniprot ID:: P20648
Molecular weight:: 114117.74

Showing metabocard for Rabeprazole (HMDB0005026)

MOL for HMDB0005026 (Rabeprazole)

3D MOL for HMDB0005026 (Rabeprazole)

3D SDF for HMDB0005026 (Rabeprazole)

3D-SDF for HMDB0005026 (Rabeprazole)

PDB for HMDB0005026 (Rabeprazole)

3D PDB for HMDB0005026 (Rabeprazole)

SMILES for HMDB0005026 (Rabeprazole)

INCHI for HMDB0005026 (Rabeprazole)

Structure for HMDB0005026 (Rabeprazole)

3D Structure for HMDB0005026 (Rabeprazole)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

Enzymes