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Showing metabocard for Methylselenopyruvate (HMDB0060490)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (2) Show 2 proteinsXML
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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-05-17 01:24:33 UTC
Update Date2023-02-21 17:30:02 UTC
HMDB IDHMDB0060490
Secondary Accession Numbers
  • HMDB60490
Metabolite Identification
Common NameMethylselenopyruvate
DescriptionMethylselenopyruvate belongs to the class of organic compounds known as alpha-keto acids and derivatives. These are organic compounds containing an aldehyde substituted with a keto group on the adjacent carbon. Methylselenopyruvate is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Data?1677000602
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0060490 (Methylselenopyruvate)

  Mrv1652308231800032D          

  8  7  0  0  0  0            999 V2000
   -1.7861    0.6187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717    0.2062    0.0000 Se  0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572    1.0312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7861    0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717   -1.0312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
M  END
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3D MOL for HMDB0060490 (Methylselenopyruvate)

HMDB0060490
     RDKit          3D
Methylselenopyruvate
 14 13  0  0  0  0  0  0  0  0999 V2000
   -3.0434    0.1348   -0.3809 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2206   -0.3502   -0.7212 Se  0  0  0  0  0  2  0  0  0  0  0  0
   -0.0253    0.3788    0.6559 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1719   -0.4802    0.7643 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0878   -1.5661    1.3743 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4142   -0.0720    0.1760 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4830    1.0390   -0.3911 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5320   -0.9302    0.2493 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6776   -0.7579   -0.2186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4806    0.7577   -1.2124 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1090    0.7594    0.5224 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2258    1.4124    0.3275 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5865    0.4753    1.6073 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2283   -0.8009   -0.4552 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  2  0
  4  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  3 12  1  0
  3 13  1  0
  8 14  1  0
M  END
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3D SDF for HMDB0060490 (Methylselenopyruvate)

  Mrv1652308231800032D          

  8  7  0  0  0  0            999 V2000
   -1.7861    0.6187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717    0.2062    0.0000 Se  0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572    1.0312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7861    0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717   -1.0312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060490

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H6O3Se/c1-8-2-3(5)4(6)7/h2H2,1H3,(H,6,7)

> <INCHI_KEY>
KCHPIRYOQIGZLW-UHFFFAOYSA-N

> <FORMULA>
C4H6O3Se

> <MOLECULAR_WEIGHT>
181.05

> <EXACT_MASS>
181.948215886

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
11.351778971123984

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-(methylselanyl)-2-oxopropanoic acid

> <ALOGPS_LOGP>
-0.47

> <JCHEM_LOGP>
0.3267

> <ALOGPS_LOGS>
-0.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
19.29770358469391

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.158429385473791

> <JCHEM_PKA_STRONGEST_BASIC>
-9.889222584139324

> <JCHEM_POLAR_SURFACE_AREA>
54.370000000000005

> <JCHEM_REFRACTIVITY>
35.7913

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.49e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-(methylselanyl)-2-oxopropanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0060490 (Methylselenopyruvate)

HMDB0060490
     RDKit          3D
Methylselenopyruvate
 14 13  0  0  0  0  0  0  0  0999 V2000
   -3.0434    0.1348   -0.3809 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2206   -0.3502   -0.7212 Se  0  0  0  0  0  2  0  0  0  0  0  0
   -0.0253    0.3788    0.6559 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1719   -0.4802    0.7643 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0878   -1.5661    1.3743 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4142   -0.0720    0.1760 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4830    1.0390   -0.3911 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5320   -0.9302    0.2493 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6776   -0.7579   -0.2186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4806    0.7577   -1.2124 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1090    0.7594    0.5224 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2258    1.4124    0.3275 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5865    0.4753    1.6073 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2283   -0.8009   -0.4552 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  2  0
  4  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  3 12  1  0
  3 13  1  0
  8 14  1  0
M  END
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PDB for HMDB0060490 (Methylselenopyruvate)

HEADER    PROTEIN                                 23-AUG-18   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-AUG-18         0                                  
HETATM    1  C   UNK     0      -3.334   1.155   0.000  0.00  0.00           C+0
HETATM    2 Se   UNK     0      -2.001   0.385   0.000  0.00  0.00          Se+0
HETATM    3  C   UNK     0      -0.667  -0.385   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.667   0.385   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.667   1.925   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       2.001  -0.385   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       3.334   0.385   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       2.001  -1.925   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for HMDB0060490 (Methylselenopyruvate)

COMPND    HMDB0060490
HETATM    1  C1  UNL     1      -3.043   0.135  -0.381  1.00  0.00           C  
HETATM    2 SE1  UNL     1      -1.221  -0.350  -0.721  1.00  0.00          SE  
HETATM    3  C2  UNL     1      -0.025   0.379   0.656  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.172  -0.480   0.764  1.00  0.00           C  
HETATM    5  O1  UNL     1       1.088  -1.566   1.374  1.00  0.00           O  
HETATM    6  C4  UNL     1       2.414  -0.072   0.176  1.00  0.00           C  
HETATM    7  O2  UNL     1       2.483   1.039  -0.391  1.00  0.00           O  
HETATM    8  O3  UNL     1       3.532  -0.930   0.249  1.00  0.00           O  
HETATM    9  H1  UNL     1      -3.678  -0.758  -0.219  1.00  0.00           H  
HETATM   10  H2  UNL     1      -3.481   0.758  -1.212  1.00  0.00           H  
HETATM   11  H3  UNL     1      -3.109   0.759   0.522  1.00  0.00           H  
HETATM   12  H4  UNL     1       0.226   1.412   0.328  1.00  0.00           H  
HETATM   13  H5  UNL     1      -0.587   0.475   1.607  1.00  0.00           H  
HETATM   14  H6  UNL     1       4.228  -0.801  -0.455  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3
CONECT    3    4   12   13
CONECT    4    5    5    6
CONECT    6    7    7    8
CONECT    8   14
END
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SMILES for HMDB0060490 (Methylselenopyruvate)

C[Se]CC(=O)C(O)=O
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INCHI for HMDB0060490 (Methylselenopyruvate)

InChI=1S/C4H6O3Se/c1-8-2-3(5)4(6)7/h2H2,1H3,(H,6,7)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
beta-MethylselenopyruvateKegg
b-MethylselenopyruvateGenerator
b-Methylselenopyruvic acidGenerator
beta-Methylselenopyruvic acidGenerator
Β-methylselenopyruvateGenerator
Β-methylselenopyruvic acidGenerator
Methylselenopyruvic acidGenerator
Chemical FormulaC4H6O3Se
Average Molecular Weight181.05
Monoisotopic Molecular Weight181.948215886
IUPAC Name3-(methylselanyl)-2-oxopropanoic acid
Traditional Name3-(methylselanyl)-2-oxopropanoic acid
CAS Registry NumberNot Available
SMILES
C[Se]CC(=O)C(O)=O
InChI Identifier
InChI=1S/C4H6O3Se/c1-8-2-3(5)4(6)7/h2H2,1H3,(H,6,7)
InChI KeyKCHPIRYOQIGZLW-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha-keto acids and derivatives. These are organic compounds containing an aldehyde substituted with a keto group on the adjacent carbon.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassKeto acids and derivatives
Sub ClassAlpha-keto acids and derivatives
Direct ParentAlpha-keto acids and derivatives
Alternative Parents
Substituents
  • Alpha-keto acid
  • Alpha-hydroxy ketone
  • Ketone
  • Selenoether
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organoselenium compound
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
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
Predicted Chromatographic Properties
Spectra
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 IDC18904
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53297415
PDB IDNot Available
ChEBI ID82049
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. Kynurenine--oxoglutarate transaminase 1
General function:
Involved in 1-aminocyclopropane-1-carboxylate synthase activity
Specific function:
Catalyzes the irreversible transamination of the L-tryptophan metabolite L-kynurenine to form kynurenic acid (KA). Metabolizes the cysteine conjugates of certain halogenated alkenes and alkanes to form reactive metabolites. Catalyzes the beta-elimination of S-conjugates and Se-conjugates of L-(seleno)cysteine, resulting in the cleavage of the C-S or C-Se bond.
Gene Name:
CCBL1
Uniprot ID:
Q16773
Molecular weight:
47874.765
Reactions
Se-Methylselenocysteine + 2-Oxo-4-methylthiobutanoic acid → Methylselenopyruvate + Methioninedetails
Enzyme Details
2. Kynurenine--oxoglutarate transaminase 3
General function:
Involved in transferase activity, transferring nitrogenous groups
Specific function:
Catalyzes the irreversible transamination of the L-tryptophan metabolite L-kynurenine to form kynurenic acid (KA). May catalyze the beta-elimination of S-conjugates and Se-conjugates of L-(seleno)cysteine, resulting in the cleavage of the C-S or C-Se bond (By similarity). Has transaminase activity towards L-kynurenine, tryptophan, phenylalanine, serine, cysteine, methionine, histidine, glutamine and asparagine with glyoxylate as an amino group acceptor (in vitro). Has lower activity with 2-oxoglutarate as amino group acceptor (in vitro) (By similarity).
Gene Name:
CCBL2
Uniprot ID:
Q6YP21
Molecular weight:
51399.855
Reactions
Se-Methylselenocysteine + 2-Oxo-4-methylthiobutanoic acid → Methylselenopyruvate + Methioninedetails