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Showing metabocard for Methylselenic acid (HMDB0060489)

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enzymes (3) Show 3 proteins
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-05-17 01:24:29 UTC
Update Date2023-02-21 17:30:02 UTC
HMDB IDHMDB0060489
Secondary Accession Numbers
  • HMDB60489
Metabolite Identification
Common NameMethylselenic acid
DescriptionMethylselenic acid, also known as methylseleninate, belongs to the class of organic compounds known as seleninic acids and derivatives. Seleninic acids and derivatives are compounds containing a seleninic acid moiety, with the general structure RSe(=O)OH. Methylselenic acid is a moderately acidic compound (based on its pKa).
Structure
Data?1677000602
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0060489 (Methylselenic acid)


  Mrv0541 05161318242D          

  4  3  0  0  0  0            999 V2000
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Se  0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  2  1  0  0  0  0
  4  3  2  0  0  0  0
M  END
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3D MOL for HMDB0060489 (Methylselenic acid)

HMDB0060489
     RDKit          3D
Methylselenic acid
  8  7  0  0  0  0  0  0  0  0999 V2000
   -1.1873   -0.2102   -0.1085 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5352    0.6636   -0.4684 Se  0  0  0  0  0  4  0  0  0  0  0  0
    0.7739    1.9353    0.5271 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8244   -0.5949   -0.1253 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4344   -0.7593   -1.0306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0598   -0.9034    0.7564 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9472    0.5252    0.2006 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4952   -0.6563   -0.8322 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  1  5  1  0
  1  6  1  0
  1  7  1  0
  4  8  1  0
M  END
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3D SDF for HMDB0060489 (Methylselenic acid)


  Mrv0541 05161318242D          

  4  3  0  0  0  0            999 V2000
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Se  0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  2  1  0  0  0  0
  4  3  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060489

> <DATABASE_NAME>
hmdb

> <SMILES>
C[Se](O)=O

> <INCHI_IDENTIFIER>
InChI=1S/CH4O2Se/c1-4(2)3/h1H3,(H,2,3)

> <INCHI_KEY>
UEQANLFPOFICBH-UHFFFAOYSA-N

> <FORMULA>
CH4O2Se

> <MOLECULAR_WEIGHT>
127.0

> <EXACT_MASS>
127.9376512

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
6.896405299481537

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methaneseleninic acid

> <ALOGPS_LOGP>
-0.95

> <JCHEM_LOGP>
-1.0135999999999998

> <ALOGPS_LOGS>
0.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.5

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
23.0681

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.01e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methaneseleninic acid

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0060489 (Methylselenic acid)

HMDB0060489
     RDKit          3D
Methylselenic acid
  8  7  0  0  0  0  0  0  0  0999 V2000
   -1.1873   -0.2102   -0.1085 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5352    0.6636   -0.4684 Se  0  0  0  0  0  4  0  0  0  0  0  0
    0.7739    1.9353    0.5271 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8244   -0.5949   -0.1253 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4344   -0.7593   -1.0306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0598   -0.9034    0.7564 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9472    0.5252    0.2006 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4952   -0.6563   -0.8322 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  1  5  1  0
  1  6  1  0
  1  7  1  0
  4  8  1  0
M  END
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PDB for HMDB0060489 (Methylselenic acid)

HEADER    PROTEIN                                 16-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-MAY-13         0                                  
HETATM    1  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -0.770   1.334   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       1.540   0.000   0.000  0.00  0.00           O+0
HETATM    4 Se   UNK     0       0.000   0.000   0.000  0.00  0.00          Se+0
CONECT    1    4                                                            
CONECT    2    4                                                            
CONECT    3    4                                                            
CONECT    4    1    2    3                                                  
MASTER        0    0    0    0    0    0    0    0    4    0    6    0
END
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3D PDB for HMDB0060489 (Methylselenic acid)

COMPND    HMDB0060489
HETATM    1  C1  UNL     1      -1.187  -0.210  -0.109  1.00  0.00           C  
HETATM    2 SE1  UNL     1       0.535   0.664  -0.468  1.00  0.00          SE  
HETATM    3  O1  UNL     1       0.774   1.935   0.527  1.00  0.00           O  
HETATM    4  O2  UNL     1       1.824  -0.595  -0.125  1.00  0.00           O  
HETATM    5  H1  UNL     1      -1.434  -0.759  -1.031  1.00  0.00           H  
HETATM    6  H2  UNL     1      -1.060  -0.903   0.756  1.00  0.00           H  
HETATM    7  H3  UNL     1      -1.947   0.525   0.201  1.00  0.00           H  
HETATM    8  H4  UNL     1       2.495  -0.656  -0.832  1.00  0.00           H  
CONECT    1    2    5    6    7
CONECT    2    3    3    4
CONECT    4    8
END
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SMILES for HMDB0060489 (Methylselenic acid)

C[Se](O)=O
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INCHI for HMDB0060489 (Methylselenic acid)

InChI=1S/CH4O2Se/c1-4(2)3/h1H3,(H,2,3)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
MethylseleninateChEBI
Methylseleninic acidGenerator
MethylselenateGenerator
Methylselenic acidMeSH
Methaneseleninic acidMeSH
Chemical FormulaCH4O2Se
Average Molecular Weight127.0
Monoisotopic Molecular Weight127.9376512
IUPAC Namemethaneseleninic acid
Traditional Namemethaneseleninic acid
CAS Registry NumberNot Available
SMILES
C[Se](O)=O
InChI Identifier
InChI=1S/CH4O2Se/c1-4(2)3/h1H3,(H,2,3)
InChI KeyUEQANLFPOFICBH-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as seleninic acids and derivatives. Seleninic acids and derivatives are compounds containing a seleninic acid moiety, with the general structure RSe(=O)OH.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassSeleninic acids and derivatives
Sub ClassNot Available
Direct ParentSeleninic acids and derivatives
Alternative Parents
Substituents
  • Seleninic acid or derivatives
  • Selenenic acid
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organoselenium compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
DispositionNot Available
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility301 g/LALOGPS
logP-0.95ALOGPS
logP-1ChemAxon
logS0.37ALOGPS
pKa (Strongest Acidic)1.5ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area37.3 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity23.07 m³·mol⁻¹ChemAxon
Polarizability6.9 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+128.16130932474
DeepCCS[M-H]-125.85430932474
DeepCCS[M-2H]-162.01130932474
DeepCCS[M+Na]+136.41730932474
AllCCS[M+H]+117.332859911
AllCCS[M+H-H2O]+113.232859911
AllCCS[M+NH4]+121.132859911
AllCCS[M+Na]+122.332859911
AllCCS[M-H]-169.832859911
AllCCS[M+Na-2H]-176.532859911
AllCCS[M+HCOO]-183.932859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Methylselenic acidC[Se](O)=O1424.3Standard polar33892256
Methylselenic acidC[Se](O)=O784.1Standard non polar33892256
Methylselenic acidC[Se](O)=O843.1Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Methylselenic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-03di-0900000000-738c5bab40812dbe3dbf2016-09-22Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Methylselenic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylselenic acid 10V, Positive-QTOFsplash10-004i-0900000000-c2249b4b1c826652f1ce2016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylselenic acid 20V, Positive-QTOFsplash10-004i-0900000000-e5486d4ba90b4e382f5c2016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylselenic acid 40V, Positive-QTOFsplash10-004i-0900000000-cbdf2df1455dc55d640b2016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylselenic acid 10V, Negative-QTOFsplash10-004i-1900000000-e1879fefae142859e17e2016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylselenic acid 20V, Negative-QTOFsplash10-004i-3900000000-1fbc5dd6c684fa8e77de2016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylselenic acid 40V, Negative-QTOFsplash10-004i-0900000000-a6230738f288f38b27b22016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylselenic acid 10V, Positive-QTOFsplash10-03di-0900000000-bb9fa0fb77cc57b595dc2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylselenic acid 20V, Positive-QTOFsplash10-01t9-0900000000-2d829f61b944a55a47422021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylselenic acid 40V, Positive-QTOFsplash10-03di-0900000000-b42052655e660ceab4b52021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylselenic acid 10V, Negative-QTOFsplash10-004i-0900000000-e76b812159d340530b922021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylselenic acid 20V, Negative-QTOFsplash10-004i-0900000000-cce7a8893676b354a80a2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylselenic acid 40V, Negative-QTOFsplash10-056r-0900000000-36fefa50db3c181f7b3a2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-04FELIX labView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC18902
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkMethaneseleninic_Acid
METLIN IDNot Available
PubChem Compound161597
PDB IDNot Available
ChEBI ID77012
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Magrane M: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. [PubMed:21447597 ]

Enzymes

Enzyme Details
1. Thioredoxin reductase 1, cytoplasmic
General function:
Involved in oxidoreductase activity
Specific function:
Isoform 1 may possess glutaredoxin activity as well as thioredoxin reductase activity and induces actin and tubulin polymerization, leading to formation of cell membrane protrusions. Isoform 4 enhances the transcriptional activity of estrogen receptors alpha and beta while isoform 5 enhances the transcriptional activity of the beta receptor only. Isoform 5 also mediates cell death induced by a combination of interferon-beta and retinoic acid.
Gene Name:
TXNRD1
Uniprot ID:
Q16881
Molecular weight:
70905.58
Reactions
NADPH + Hydrogen Ion + Methylselenic acid → NADP + Water + Methaneselenoldetails
Enzyme Details
2. Thioredoxin reductase 2, mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
Maintains thioredoxin in a reduced state. Implicated in the defenses against oxidative stress. May play a role in redox-regulated cell signaling.
Gene Name:
TXNRD2
Uniprot ID:
Q9NNW7
Molecular weight:
56506.275
Reactions
NADPH + Hydrogen Ion + Methylselenic acid → NADP + Water + Methaneselenoldetails
Enzyme Details
3. Thioredoxin reductase 3
General function:
Involved in oxidoreductase activity
Specific function:
Displays thioredoxin reductase, glutaredoxin and glutathione reductase activities. Catalyzes disulfide bond isomerization. Promotes disulfide bond formation between GPX4 and various sperm proteins and may play a role in sperm maturation by promoting formation of sperm structural components (By similarity).
Gene Name:
TXNRD3
Uniprot ID:
Q86VQ6
Molecular weight:
66600.92
Reactions
NADPH + Hydrogen Ion + Methylselenic acid → NADP + Water + Methaneselenoldetails