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Showing metabocard for 2,3-Dihydroxyvaleric acid (HMDB0000421)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2022-09-22 18:35:06 UTC
HMDB IDHMDB0000421
Secondary Accession Numbers
  • HMDB00421
Metabolite Identification
Common Name2,3-Dihydroxyvaleric acid
Description2,3-Dihydroxyvaleric acid (DHVA) belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group. This compound has been detected in extracts from the purple carrot (https://doi.org/10.3390/app10238493). It is likely a hydroxylation derivative of the more common 2-hydroxyvaleric acid (an algal metabolite derived from a valeric acid) or 3-hydroxyvaleric acid (a 5-carbon ketone body made from odd carbon fatty acids in the liver). Very little is known about the origin of this particular hydroxy fatty acid.
Structure
Data?1582752130
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000421 (2,3-Dihydroxyvaleric acid)

2,3-dihydroxy-Valeric acid.mol
  Mrv1652305261923552D          

  9  8  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   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7862    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   -0.2062    0.0000 O   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
    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
  4  5  1  0  0  0  0
  1  6  2  0  0  0  0
  1  7  1  0  0  0  0
  3  8  1  0  0  0  0
  2  9  1  0  0  0  0
M  END
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3D MOL for HMDB0000421 (2,3-Dihydroxyvaleric acid)

HMDB0000421
     RDKit          3D
2,3-Dihydroxyvaleric acid
 19 18  0  0  0  0  0  0  0  0999 V2000
    2.1987    0.6634    0.8784 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6765    0.4879    0.9959 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3055   -0.4759   -0.1005 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6426    0.0104   -1.3592 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1380   -0.8706   -0.1084 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2911   -1.8591   -1.0810 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0654    0.2169   -0.4254 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8200    0.1762   -1.4175 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1049    1.3409    0.4160 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6958   -0.2445    1.2558 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4113    0.7290   -0.2027 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5419    1.5712    1.3793 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5179    0.0318    1.9942 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1633    1.4435    0.9596 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9001   -1.4032    0.0673 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4636   -0.4103   -1.6924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4341   -1.3636    0.8607 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7040   -1.7331   -1.8610 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9597    1.6891    0.8112 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
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  0
  4 16  1  0
  5 17  1  0
  6 18  1  0
  9 19  1  0
M  END
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3D SDF for HMDB0000421 (2,3-Dihydroxyvaleric acid)

2,3-dihydroxy-Valeric acid.mol
  Mrv1652305261923552D          

  9  8  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   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7862    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   -0.2062    0.0000 O   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
    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
  4  5  1  0  0  0  0
  1  6  2  0  0  0  0
  1  7  1  0  0  0  0
  3  8  1  0  0  0  0
  2  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000421

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O4/c1-2-3(6)4(7)5(8)9/h3-4,6-7H,2H2,1H3,(H,8,9)

> <INCHI_KEY>
CJXCLBPFKGZXJP-UHFFFAOYSA-N

> <FORMULA>
C5H10O4

> <MOLECULAR_WEIGHT>
134.1305

> <EXACT_MASS>
134.057908808

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
12.717206006383734

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3-dihydroxypentanoic acid

> <ALOGPS_LOGP>
-0.87

> <JCHEM_LOGP>
-0.579642065

> <ALOGPS_LOGS>
0.42

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.264842121326641

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.8016080976510094

> <JCHEM_PKA_STRONGEST_BASIC>
-3.254534149492307

> <JCHEM_POLAR_SURFACE_AREA>
77.76

> <JCHEM_REFRACTIVITY>
29.326299999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.49e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3-dihydroxyvaleric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0000421 (2,3-Dihydroxyvaleric acid)

HMDB0000421
     RDKit          3D
2,3-Dihydroxyvaleric acid
 19 18  0  0  0  0  0  0  0  0999 V2000
    2.1987    0.6634    0.8784 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6765    0.4879    0.9959 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3055   -0.4759   -0.1005 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6426    0.0104   -1.3592 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1380   -0.8706   -0.1084 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2911   -1.8591   -1.0810 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0654    0.2169   -0.4254 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8200    0.1762   -1.4175 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1049    1.3409    0.4160 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6958   -0.2445    1.2558 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4113    0.7290   -0.2027 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5419    1.5712    1.3793 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5179    0.0318    1.9942 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1633    1.4435    0.9596 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9001   -1.4032    0.0673 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4636   -0.4103   -1.6924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4341   -1.3636    0.8607 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7040   -1.7331   -1.8610 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9597    1.6891    0.8112 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
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  0
  4 16  1  0
  5 17  1  0
  6 18  1  0
  9 19  1  0
M  END
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PDB for HMDB0000421 (2,3-Dihydroxyvaleric acid)

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 2,3-dihydroxy-Valeric acid.mol                    
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         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  C   UNK     0      -3.334   0.385   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.001   1.925   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
HETATM    9  O   UNK     0       0.667  -1.925   0.000  0.00  0.00           O+0
CONECT    1    2    6    7                                                  
CONECT    2    1    3    9                                                  
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4                                                            
CONECT    6    1                                                            
CONECT    7    1                                                            
CONECT    8    3                                                            
CONECT    9    2                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for HMDB0000421 (2,3-Dihydroxyvaleric acid)

COMPND    HMDB0000421
HETATM    1  C1  UNL     1       2.199   0.663   0.878  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.677   0.488   0.996  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.305  -0.476  -0.100  1.00  0.00           C  
HETATM    4  O1  UNL     1       0.643   0.010  -1.359  1.00  0.00           O  
HETATM    5  C4  UNL     1      -1.138  -0.871  -0.108  1.00  0.00           C  
HETATM    6  O2  UNL     1      -1.291  -1.859  -1.081  1.00  0.00           O  
HETATM    7  C5  UNL     1      -2.065   0.217  -0.425  1.00  0.00           C  
HETATM    8  O3  UNL     1      -2.820   0.176  -1.417  1.00  0.00           O  
HETATM    9  O4  UNL     1      -2.105   1.341   0.416  1.00  0.00           O  
HETATM   10  H1  UNL     1       2.696  -0.245   1.256  1.00  0.00           H  
HETATM   11  H2  UNL     1       2.411   0.729  -0.203  1.00  0.00           H  
HETATM   12  H3  UNL     1       2.542   1.571   1.379  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.518   0.032   1.994  1.00  0.00           H  
HETATM   14  H5  UNL     1       0.163   1.443   0.960  1.00  0.00           H  
HETATM   15  H6  UNL     1       0.900  -1.403   0.067  1.00  0.00           H  
HETATM   16  H7  UNL     1       1.464  -0.410  -1.692  1.00  0.00           H  
HETATM   17  H8  UNL     1      -1.434  -1.364   0.861  1.00  0.00           H  
HETATM   18  H9  UNL     1      -0.704  -1.733  -1.861  1.00  0.00           H  
HETATM   19  H10 UNL     1      -2.960   1.689   0.811  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3   13   14
CONECT    3    4    5   15
CONECT    4   16
CONECT    5    6    7   17
CONECT    6   18
CONECT    7    8    8    9
CONECT    9   19
END
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SMILES for HMDB0000421 (2,3-Dihydroxyvaleric acid)

CCC(O)C(O)C(O)=O
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INCHI for HMDB0000421 (2,3-Dihydroxyvaleric acid)

InChI=1S/C5H10O4/c1-2-3(6)4(7)5(8)9/h3-4,6-7H,2H2,1H3,(H,8,9)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2,3-DihydroxyvalerateGenerator
2,3-Dihydroxy-valerateHMDB
2,3-Dihydroxy-valeric acidHMDB
Chemical FormulaC5H10O4
Average Molecular Weight134.1305
Monoisotopic Molecular Weight134.057908808
IUPAC Name2,3-dihydroxypentanoic acid
Traditional Name2,3-dihydroxyvaleric acid
CAS Registry Number26386-47-0
SMILES
CCC(O)C(O)C(O)=O
InChI Identifier
InChI=1S/C5H10O4/c1-2-3(6)4(7)5(8)9/h3-4,6-7H,2H2,1H3,(H,8,9)
InChI KeyCJXCLBPFKGZXJP-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentHydroxy fatty acids
Alternative Parents
Substituents
  • Beta-hydroxy acid
  • Branched fatty acid
  • Hydroxy fatty acid
  • Short-chain hydroxy acid
  • Methyl-branched fatty acid
  • Monosaccharide
  • Hydroxy acid
  • Alpha-hydroxy acid
  • Secondary alcohol
  • 1,2-diol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Organic oxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological role
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 Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedAdult (>18 years old)BothAsthma details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothAsthma details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022035
KNApSAcK IDNot Available
Chemspider ID13451358
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5410
PubChem Compound20848966
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceKogl, Fritz; Duisberg, Herwarth; Erxleben, Hanni. Fungus poisons. I. Muscarine. I. Ann. (1931), 489 156-92.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Holmes E, Foxall PJ, Spraul M, Farrant RD, Nicholson JK, Lindon JC: 750 MHz 1H NMR spectroscopy characterisation of the complex metabolic pattern of urine from patients with inborn errors of metabolism: 2-hydroxyglutaric aciduria and maple syrup urine disease. J Pharm Biomed Anal. 1997 Jul;15(11):1647-59. [PubMed:9260660 ]