Hmdb loader

Showing metabocard for 2-Ketobutyric acid (HMDB0000005)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (21) Show 21 proteinsXML
enzymes (21) Show 21 proteins
Show more...Show more...Show more...Show more...Show more...
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:14:27 UTC
HMDB IDHMDB0000005
Secondary Accession Numbers
  • HMDB00005
  • HMDB0006544
  • HMDB06544
Metabolite Identification
Common Name2-Ketobutyric acid
Description2-Ketobutyric acid, also known as alpha-ketobutyrate or 2-oxobutyrate, belongs to the class of organic compounds known as short-chain keto acids and derivatives. These are keto acids with an alkyl chain the contains less than 6 carbon atoms. 2-Ketobutyric acid is a substance that is involved in the metabolism of many amino acids (glycine, methionine, valine, leucine, serine, threonine, isoleucine) as well as propanoate metabolism and C-5 branched dibasic acid metabolism. It is also one of the degradation products of threonine. It can be converted into propionyl-CoA (and subsequently methylmalonyl CoA, which can be converted into succinyl CoA, a citric acid cycle intermediate), and thus enter the citric acid cycle. More specifically, 2-ketobutyric acid is a product of the lysis of cystathionine.
Structure
Data?1676999667
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000005 (2-Ketobutyric acid)

      
  Mrv1652309032023492D          

  7  6  0  0  0  0            999 V2000
    2.4602    0.5082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7456    0.9207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0312    0.5082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0312   -0.3167    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3167    0.9207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3977    0.5082    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3167    1.7457    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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
M  END
Download

3D MOL for HMDB0000005 (2-Ketobutyric acid)

HMDB0000005
     RDKit          3D
2-Ketobutyric acid
 13 12  0  0  0  0  0  0  0  0999 V2000
   -1.7055   -0.6699    0.3833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8926    0.4866   -0.1627 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4457    0.0723   -0.6071 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5739   -0.4456   -1.7421 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6340    0.2367    0.2136 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5055    0.7589    1.3554 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9003   -0.1376   -0.1660 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0786   -1.5747    0.5457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5302   -0.9681   -0.2918 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1732   -0.4066    1.3657 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4677    0.9348   -1.0181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8426    1.2620    0.6348 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6309    0.4514   -0.5107 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  7 13  1  0
M  END
Download

3D SDF for HMDB0000005 (2-Ketobutyric acid)

      
  Mrv1652309032023492D          

  7  6  0  0  0  0            999 V2000
    2.4602    0.5082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7456    0.9207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0312    0.5082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0312   -0.3167    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3167    0.9207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3977    0.5082    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3167    1.7457    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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000005

> <DATABASE_NAME>
hmdb

> <SMILES>
CCC(=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H6O3/c1-2-3(5)4(6)7/h2H2,1H3,(H,6,7)

> <INCHI_KEY>
TYEYBOSBBBHJIV-UHFFFAOYSA-N

> <FORMULA>
C4H6O3

> <MOLECULAR_WEIGHT>
102.0886

> <EXACT_MASS>
102.031694058

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
9.1994455800129

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-oxobutanoic acid

> <ALOGPS_LOGP>
0.07

> <JCHEM_LOGP>
0.7664098003333332

> <ALOGPS_LOGS>
-0.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1869864284881544

> <JCHEM_PKA_STRONGEST_BASIC>
-9.650960797412663

> <JCHEM_POLAR_SURFACE_AREA>
54.37

> <JCHEM_REFRACTIVITY>
22.616600000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.92e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-oxobutanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0000005 (2-Ketobutyric acid)

HMDB0000005
     RDKit          3D
2-Ketobutyric acid
 13 12  0  0  0  0  0  0  0  0999 V2000
   -1.7055   -0.6699    0.3833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8926    0.4866   -0.1627 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4457    0.0723   -0.6071 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5739   -0.4456   -1.7421 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6340    0.2367    0.2136 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5055    0.7589    1.3554 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9003   -0.1376   -0.1660 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0786   -1.5747    0.5457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5302   -0.9681   -0.2918 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1732   -0.4066    1.3657 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4677    0.9348   -1.0181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8426    1.2620    0.6348 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6309    0.4514   -0.5107 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  7 13  1  0
M  END
Download

PDB for HMDB0000005 (2-Ketobutyric acid)

HEADER    PROTEIN                                 03-SEP-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-20         0                                  
HETATM    1  C   UNK     0       4.592   0.949   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.258   1.719   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.925   0.949   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.925  -0.591   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.591   1.719   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -0.742   0.949   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.591   3.259   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
Download

3D PDB for HMDB0000005 (2-Ketobutyric acid)

COMPND    HMDB0000005
HETATM    1  C1  UNL     1      -1.706  -0.670   0.383  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.893   0.487  -0.163  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.446   0.072  -0.607  1.00  0.00           C  
HETATM    4  O1  UNL     1       0.574  -0.446  -1.742  1.00  0.00           O  
HETATM    5  C4  UNL     1       1.634   0.237   0.214  1.00  0.00           C  
HETATM    6  O2  UNL     1       1.505   0.759   1.355  1.00  0.00           O  
HETATM    7  O3  UNL     1       2.900  -0.138  -0.166  1.00  0.00           O  
HETATM    8  H1  UNL     1      -1.079  -1.575   0.546  1.00  0.00           H  
HETATM    9  H2  UNL     1      -2.530  -0.968  -0.292  1.00  0.00           H  
HETATM   10  H3  UNL     1      -2.173  -0.407   1.366  1.00  0.00           H  
HETATM   11  H4  UNL     1      -1.468   0.935  -1.018  1.00  0.00           H  
HETATM   12  H5  UNL     1      -0.843   1.262   0.635  1.00  0.00           H  
HETATM   13  H6  UNL     1       3.631   0.451  -0.511  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3   11   12
CONECT    3    4    4    5
CONECT    5    6    6    7
CONECT    7   13
END
Download

SMILES for HMDB0000005 (2-Ketobutyric acid)

CCC(=O)C(O)=O
Download

INCHI for HMDB0000005 (2-Ketobutyric acid)

InChI=1S/C4H6O3/c1-2-3(5)4(6)7/h2H2,1H3,(H,6,7)
Download
View in JSmolView Stereo Labels
Synonyms
Chemical FormulaC4H6O3
Average Molecular Weight102.0886
Monoisotopic Molecular Weight102.031694058
IUPAC Name2-oxobutanoic acid
Traditional Name2-oxobutanoic acid
CAS Registry Number600-18-0
SMILES
CCC(=O)C(O)=O
InChI Identifier
InChI=1S/C4H6O3/c1-2-3(5)4(6)7/h2H2,1H3,(H,6,7)
InChI KeyTYEYBOSBBBHJIV-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as short-chain keto acids and derivatives. These are keto acids with an alkyl chain the contains less than 6 carbon atoms.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassKeto acids and derivatives
Sub ClassShort-chain keto acids and derivatives
Direct ParentShort-chain keto acids and derivatives
Alternative Parents
Substituents
  • Short-chain keto acid
  • Alpha-keto acid
  • Alpha-hydroxy ketone
  • Ketone
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point33 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility119 mg/mLNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Saliva
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected and Quantified6.564 +/- 7.802 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Eosinophilic esophagitis
    • Analysis of 30 no...
 details
Associated Disorders and Diseases
Disease References
Eosinophilic esophagitis
  1. Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work). NA.
Associated OMIM IDs
DrugBank IDDB04553
Phenol Explorer Compound IDNot Available
FooDB IDFDB030356
KNApSAcK IDC00019675
Chemspider ID57
KEGG Compound IDC00109
BioCyc ID2-OXOBUTANOATE
BiGG ID33889
Wikipedia LinkAlpha-Ketobutyric_acid
METLIN IDNot Available
PubChem Compound58
PDB IDNot Available
ChEBI ID30831
Food Biomarker OntologyNot Available
VMH ID2OBUT
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceFigge, Rainer; Lux, Fabien; Raynaud, Celine; Soucaille, Philippe. Production of a-ketobutyrate by engineered Escherichia coli.PCT Int. Appl. (2006), 31pp.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Sprague CL, Elfarra AA: Detection of carboxylic acids and inhibition of hippuric acid formation in rats treated with 3-butene-1,2-diol, a major metabolite of 1,3-butadiene. Drug Metab Dispos. 2003 Aug;31(8):986-92. [PubMed:12867486 ]
  2. Yaegaki K, Sanada K: Biochemical and clinical factors influencing oral malodor in periodontal patients. J Periodontol. 1992 Sep;63(9):783-9. [PubMed:1474480 ]
  3. Yaegaki K, Sanada K: Effects of a two-phase oil-water mouthwash on halitosis. Clin Prev Dent. 1992 Jan-Feb;14(1):5-9. [PubMed:1499240 ]
  4. Yang W, Roth KS: Defect in alpha-ketobutyrate metabolism: a new inborn error. Clin Chim Acta. 1985 Jan 30;145(2):173-82. [PubMed:3918815 ]

Only showing the first 10 proteins. There are 21 proteins in total.

Show all enzymes and transporters

Enzymes

Enzyme Details
1. Pyruvate dehydrogenase E1 component subunit beta, mitochondrial
General function:
Involved in catalytic activity
Specific function:
The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2), and thereby links the glycolytic pathway to the tricarboxylic cycle.
Gene Name:
PDHB
Uniprot ID:
P11177
Molecular weight:
39233.1
References
  1. Paxton R, Scislowski PW, Davis EJ, Harris RA: Role of branched-chain 2-oxo acid dehydrogenase and pyruvate dehydrogenase in 2-oxobutyrate metabolism. Biochem J. 1986 Mar 1;234(2):295-303. [PubMed:3718468 ]
Enzyme Details
2. Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial
General function:
Involved in oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
Specific function:
The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2), and thereby links the glycolytic pathway to the tricarboxylic cycle.
Gene Name:
PDHA1
Uniprot ID:
P08559
Molecular weight:
43295.255
References
  1. Paxton R, Scislowski PW, Davis EJ, Harris RA: Role of branched-chain 2-oxo acid dehydrogenase and pyruvate dehydrogenase in 2-oxobutyrate metabolism. Biochem J. 1986 Mar 1;234(2):295-303. [PubMed:3718468 ]
Enzyme Details
3. Pyruvate dehydrogenase E1 component subunit alpha, testis-specific form, mitochondrial
General function:
Involved in oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
Specific function:
The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2), and thereby links the glycolytic pathway to the tricarboxylic cycle.
Gene Name:
PDHA2
Uniprot ID:
P29803
Molecular weight:
42932.855
References
  1. Paxton R, Scislowski PW, Davis EJ, Harris RA: Role of branched-chain 2-oxo acid dehydrogenase and pyruvate dehydrogenase in 2-oxobutyrate metabolism. Biochem J. 1986 Mar 1;234(2):295-303. [PubMed:3718468 ]
Enzyme Details
4. 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial
General function:
Involved in catalytic activity
Specific function:
The branched-chain alpha-keto dehydrogenase complex catalyzes the overall conversion of alpha-keto acids to acyl-CoA and CO(2). It contains multiple copies of three enzymatic components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3).
Gene Name:
BCKDHB
Uniprot ID:
P21953
Molecular weight:
43122.065
Enzyme Details
5. 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial
General function:
Involved in oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
Specific function:
The branched-chain alpha-keto dehydrogenase complex catalyzes the overall conversion of alpha-keto acids to acyl-CoA and CO(2). It contains multiple copies of three enzymatic components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3).
Gene Name:
BCKDHA
Uniprot ID:
P12694
Molecular weight:
50470.58
Enzyme Details
6. 2-oxoglutarate dehydrogenase, mitochondrial
General function:
Involved in oxoglutarate dehydrogenase (succinyl-transferring) activity
Specific function:
The 2-oxoglutarate dehydrogenase complex catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). It contains multiple copies of three enzymatic components: 2-oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3).
Gene Name:
OGDH
Uniprot ID:
Q02218
Molecular weight:
48179.59
Enzyme Details
7. Cystathionine gamma-lyase
General function:
Involved in pyridoxal phosphate binding
Specific function:
Catalyzes the last step in the trans-sulfuration pathway from methionine to cysteine. Has broad substrate specificity. Converts cystathionine to cysteine, ammonia and 2-oxobutanoate. Converts two cysteine molecules to lanthionine and hydrogen sulfide. Can also accept homocysteine as substrate. Specificity depends on the levels of the endogenous substrates. Generates the endogenous signaling molecule hydrogen sulfide (H2S), and so contributes to the regulation of blood pressure. Acts as a cysteine-protein sulfhydrase by mediating sulfhydration of target proteins: sulfhydration consists of converting -SH groups into -SSH on specific cysteine residues of target proteins such as GAPDH, PTPN1 and NF-kappa-B subunit RELA, thereby regulating their function.
Gene Name:
CTH
Uniprot ID:
P32929
Molecular weight:
41259.91
Reactions
L-Cystathionine + Water → L-Cysteine + Ammonia + 2-Ketobutyric aciddetails
Selenomethionine + Water → Methaneselenol + Ammonia + 2-Ketobutyric aciddetails
Selenocystathionine + Water → Selenocysteine + Ammonia + 2-Ketobutyric aciddetails
Enzyme Details
8. L-serine dehydratase/L-threonine deaminase
General function:
Involved in catalytic activity
Specific function:
Not Available
Gene Name:
SDS
Uniprot ID:
P20132
Molecular weight:
34625.105
Reactions
L-Threonine → 2-Ketobutyric acid + Ammoniadetails
Enzyme Details
9. L-lactate dehydrogenase A-like 6A
General function:
Involved in oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
Specific function:
Displays an lactate dehydrogenase activity. Significantly increases the transcriptional activity of JUN, when overexpressed.
Gene Name:
LDHAL6A
Uniprot ID:
Q6ZMR3
Molecular weight:
36507.015
Reactions
2-Hydroxybutyric acid + NAD → 2-Ketobutyric acid + NADH + Hydrogen Iondetails
Enzyme Details
10. Urocanate hydratase
General function:
Involved in urocanate hydratase activity
Specific function:
Not Available
Gene Name:
UROC1
Uniprot ID:
Q96N76
Molecular weight:
80911.275

Only showing the first 10 proteins. There are 21 proteins in total.

Show all enzymes and transporters