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Showing metabocard for 2,4-Dihydroxybutanoic acid (HMDB0000360)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:14:45 UTC
HMDB IDHMDB0000360
Secondary Accession Numbers
  • HMDB00360
Metabolite Identification
Common Name2,4-Dihydroxybutanoic acid
Description2,4-Dihydroxybutanoic acid, also known as 2,4-dihydroxybutyrate or 3-deoxytetronate, belongs to the class of organic compounds known as short-chain hydroxy acids and derivatives. These are hydroxy acids with an alkyl chain the contains less than 6 carbon atoms. 2,4-Dihydroxybutanoic acid has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make 2,4-dihydroxybutanoic acid a potential biomarker for the consumption of these foods. 2,4-Dihydroxybutanoic acid is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a small amount of articles have been published on 2,4-Dihydroxybutanoic acid.
Structure
Data?1676999685
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000360 (2,4-Dihydroxybutanoic acid)

3-Deoxytetronic acid  .mol
  Mrv0541 02231218282D          

  8  7  0  0  0  0            999 V2000
    1.0717    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -0.2063    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
   -1.0717   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717    1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7862   -0.2063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7862    0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -1.0313    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
  1  5  2  0  0  0  0
  1  6  1  0  0  0  0
  4  7  1  0  0  0  0
  2  8  1  0  0  0  0
M  END
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3D MOL for HMDB0000360 (2,4-Dihydroxybutanoic acid)

HMDB0000360
     RDKit          3D
2,4-Dihydroxybutanoic acid
 16 15  0  0  0  0  0  0  0  0999 V2000
   -2.9033   -0.9172   -0.2938 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0155   -0.0383   -0.0669 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3803    1.2764   -0.2456 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6392   -0.3863    0.3722 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5643   -1.7608    0.4650 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3211    0.1545   -0.6384 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7591   -0.1336   -0.3064 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1697    0.3953    0.8959 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8500    2.0598    0.1155 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4878    0.1200    1.3516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3695   -1.9977    1.4032 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1177    1.2304   -0.7930 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1117   -0.3458   -1.6155 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3770    0.2382   -1.1579 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8890   -1.2352   -0.2999 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4645    1.3403    0.8140 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  3  9  1  0
  4 10  1  0
  5 11  1  0
  6 12  1  0
  6 13  1  0
  7 14  1  0
  7 15  1  0
  8 16  1  0
M  END
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3D SDF for HMDB0000360 (2,4-Dihydroxybutanoic acid)

3-Deoxytetronic acid  .mol
  Mrv0541 02231218282D          

  8  7  0  0  0  0            999 V2000
    1.0717    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -0.2063    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
   -1.0717   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717    1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7862   -0.2063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7862    0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -1.0313    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
  1  5  2  0  0  0  0
  1  6  1  0  0  0  0
  4  7  1  0  0  0  0
  2  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000360

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H8O4/c5-2-1-3(6)4(7)8/h3,5-6H,1-2H2,(H,7,8)

> <INCHI_KEY>
UFYGCFHQAXXBCF-UHFFFAOYSA-N

> <FORMULA>
C4H8O4

> <MOLECULAR_WEIGHT>
120.1039

> <EXACT_MASS>
120.042258744

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
10.933480891022622

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,4-dihydroxybutanoic acid

> <ALOGPS_LOGP>
-1.46

> <JCHEM_LOGP>
-1.458779745666667

> <ALOGPS_LOGS>
0.77

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.20091433487325

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.669896389811606

> <JCHEM_PKA_STRONGEST_BASIC>
-2.418943130539679

> <JCHEM_POLAR_SURFACE_AREA>
77.76

> <JCHEM_REFRACTIVITY>
25.2489

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.00e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,4-dihydroxybutyric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0000360 (2,4-Dihydroxybutanoic acid)

HMDB0000360
     RDKit          3D
2,4-Dihydroxybutanoic acid
 16 15  0  0  0  0  0  0  0  0999 V2000
   -2.9033   -0.9172   -0.2938 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0155   -0.0383   -0.0669 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3803    1.2764   -0.2456 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6392   -0.3863    0.3722 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5643   -1.7608    0.4650 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3211    0.1545   -0.6384 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7591   -0.1336   -0.3064 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1697    0.3953    0.8959 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8500    2.0598    0.1155 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4878    0.1200    1.3516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3695   -1.9977    1.4032 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1177    1.2304   -0.7930 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1117   -0.3458   -1.6155 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3770    0.2382   -1.1579 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8890   -1.2352   -0.2999 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4645    1.3403    0.8140 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  3  9  1  0
  4 10  1  0
  5 11  1  0
  6 12  1  0
  6 13  1  0
  7 14  1  0
  7 15  1  0
  8 16  1  0
M  END
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PDB for HMDB0000360 (2,4-Dihydroxybutanoic acid)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 3-Deoxytetronic acid  .mol                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0       2.001   0.385   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.667  -0.385   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.667   0.385   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.001  -0.385   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.001   1.925   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       3.334  -0.385   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -3.334   0.385   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.667  -1.925   0.000  0.00  0.00           O+0
CONECT    1    2    5    6                                                  
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    7                                                       
CONECT    5    1                                                            
CONECT    6    1                                                            
CONECT    7    4                                                            
CONECT    8    2                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for HMDB0000360 (2,4-Dihydroxybutanoic acid)

COMPND    HMDB0000360
HETATM    1  O1  UNL     1      -2.903  -0.917  -0.294  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.015  -0.038  -0.067  1.00  0.00           C  
HETATM    3  O2  UNL     1      -2.380   1.276  -0.246  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.639  -0.386   0.372  1.00  0.00           C  
HETATM    5  O3  UNL     1      -0.564  -1.761   0.465  1.00  0.00           O  
HETATM    6  C3  UNL     1       0.321   0.154  -0.638  1.00  0.00           C  
HETATM    7  C4  UNL     1       1.759  -0.134  -0.306  1.00  0.00           C  
HETATM    8  O4  UNL     1       2.170   0.395   0.896  1.00  0.00           O  
HETATM    9  H1  UNL     1      -1.850   2.060   0.116  1.00  0.00           H  
HETATM   10  H2  UNL     1      -0.488   0.120   1.352  1.00  0.00           H  
HETATM   11  H3  UNL     1      -0.370  -1.998   1.403  1.00  0.00           H  
HETATM   12  H4  UNL     1       0.118   1.230  -0.793  1.00  0.00           H  
HETATM   13  H5  UNL     1       0.112  -0.346  -1.616  1.00  0.00           H  
HETATM   14  H6  UNL     1       2.377   0.238  -1.158  1.00  0.00           H  
HETATM   15  H7  UNL     1       1.889  -1.235  -0.300  1.00  0.00           H  
HETATM   16  H8  UNL     1       2.464   1.340   0.814  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3    9
CONECT    4    5    6   10
CONECT    5   11
CONECT    6    7   12   13
CONECT    7    8   14   15
CONECT    8   16
END
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SMILES for HMDB0000360 (2,4-Dihydroxybutanoic acid)

OCCC(O)C(O)=O
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INCHI for HMDB0000360 (2,4-Dihydroxybutanoic acid)

InChI=1S/C4H8O4/c5-2-1-3(6)4(7)8/h3,5-6H,1-2H2,(H,7,8)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2,4-Dihydroxybutyric acidChEBI
2,4-DihydroxybutyrateGenerator
2,4-DihydroxybutanoateGenerator
2,4-Dihydroxy-butyrateHMDB
2,4-Dihydroxy-butyric acidHMDB
3-DeoxytetronateHMDB
3-Deoxytetronic acidHMDB
2,4-Dihydroxy-butanoateHMDB
Chemical FormulaC4H8O4
Average Molecular Weight120.1039
Monoisotopic Molecular Weight120.042258744
IUPAC Name2,4-dihydroxybutanoic acid
Traditional Name2,4-dihydroxybutyric acid
CAS Registry Number1518-62-3
SMILES
OCCC(O)C(O)=O
InChI Identifier
InChI=1S/C4H8O4/c5-2-1-3(6)4(7)8/h3,5-6H,1-2H2,(H,7,8)
InChI KeyUFYGCFHQAXXBCF-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as short-chain hydroxy acids and derivatives. These are hydroxy acids with an alkyl chain the contains less than 6 carbon atoms.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassHydroxy acids and derivatives
Sub ClassShort-chain hydroxy acids and derivatives
Direct ParentShort-chain hydroxy acids and derivatives
Alternative Parents
Substituents
  • Short-chain hydroxy acid
  • Alpha-hydroxy acid
  • Monosaccharide
  • Fatty acid
  • Secondary alcohol
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Organic oxide
  • Organic oxygen compound
  • Alcohol
  • Carbonyl group
  • Organooxygen compound
  • Primary alcohol
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
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 Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothBladder cancer details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB021980
KNApSAcK IDC00052108
Chemspider ID167259
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5349
PubChem Compound192742
PDB IDNot Available
ChEBI ID86348
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceRadej, Z.; Kristofova, Z. Hydroxy acid and lactone fraction of black liquor. Papir a Celuloza (1964), 19(6), 152-3.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Guneral F, Bachmann C: Age-related reference values for urinary organic acids in a healthy Turkish pediatric population. Clin Chem. 1994 Jun;40(6):862-6. [PubMed:8087979 ]
  2. Thompson JA, Markey SP, Fennessey PV: Gas-chromatographic/mass-spectrometric identification and quantitation of tetronic and deoxytetronic acids in urine from normal adults and neonates. Clin Chem. 1975 Dec;21(13):1892-8. [PubMed:1192581 ]
  3. Brown GK, Cromby CH, Manning NJ, Pollitt RJ: Urinary organic acids in succinic semialdehyde dehydrogenase deficiency: evidence of alpha-oxidation of 4-hydroxybutyric acid, interaction of succinic semialdehyde with pyruvate dehydrogenase and possible secondary inhibition of mitochondrial beta-oxidation. J Inherit Metab Dis. 1987;10(4):367-75. [PubMed:3126356 ]