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Showing metabocard for 2,3-dihydroxy-3-methylvalerate (HMDB0304038)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 06:38:42 UTC
Update Date2021-09-24 06:38:42 UTC
HMDB IDHMDB0304038
Secondary Accession NumbersNone
Metabolite Identification
Common Name2,3-dihydroxy-3-methylvalerate
Description2,3-dihydroxy-3-methylvalerate is a member of the class of compounds known as hydroxy fatty acids. Hydroxy fatty acids are fatty acids in which the chain bears a hydroxyl group. Thus, 2,3-dihydroxy-3-methylvalerate is considered to be a fatty acid lipid molecule. 2,3-dihydroxy-3-methylvalerate is soluble (in water) and a weakly acidic compound (based on its pKa). 2,3-dihydroxy-3-methylvalerate can be found in a number of food items such as jostaberry, spelt, roman camomile, and common pea, which makes 2,3-dihydroxy-3-methylvalerate a potential biomarker for the consumption of these food products.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304038 (2,3-dihydroxy-3-methylvalerate)

  Mrv1533005021511012D          

 10  9  0  0  0  0            999 V2000
    0.8250    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
M  END
Download

3D MOL for HMDB0304038 (2,3-dihydroxy-3-methylvalerate)

HMDB0304038
     RDKit          3D
2,3-dihydroxy-3-methylvalerate
 22 21  0  0  0  0  0  0  0  0999 V2000
   -1.9280    0.8483    1.0315 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5896   -0.2034   -0.0176 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1753    0.0402   -0.5672 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1205   -1.0097   -1.5925 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0205    1.3319   -1.0073 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7434   -0.2194    0.6254 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5161   -1.5378    0.9940 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1395    0.0828    0.3489 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0553   -0.7694    0.4354 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5109    1.3618   -0.0303 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5519    0.5766    2.0269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5967    1.8586    0.7350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0385    0.8760    1.1091 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3470   -0.1372   -0.7972 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6236   -1.1775    0.5132 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9991   -0.6953   -2.2096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7243   -1.1817   -2.2933 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3757   -1.9563   -1.0621 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4033    1.4027   -1.9355 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3952    0.4937    1.4245 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7833   -1.7393    1.9245 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3594    1.7543    0.3443 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
  3  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  0
  2 15  1  0
  4 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  6 20  1  0
  7 21  1  0
 10 22  1  0
M  END
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3D SDF for HMDB0304038 (2,3-dihydroxy-3-methylvalerate)

  Mrv1533005021511012D          

 10  9  0  0  0  0            999 V2000
    0.8250    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0304038

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O4/c1-3-6(2,10)4(7)5(8)9/h4,7,10H,3H2,1-2H3,(H,8,9)

> <INCHI_KEY>
PDGXJDXVGMHUIR-UHFFFAOYSA-N

> <FORMULA>
C6H12O4

> <MOLECULAR_WEIGHT>
148.158

> <EXACT_MASS>
148.073558866

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
14.394533141567326

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3-dihydroxy-3-methylpentanoic acid

> <ALOGPS_LOGP>
-0.44

> <JCHEM_LOGP>
-0.2990653966666666

> <ALOGPS_LOGS>
0.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.109092933547867

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.930562552523404

> <JCHEM_PKA_STRONGEST_BASIC>
-3.320314291594766

> <JCHEM_POLAR_SURFACE_AREA>
77.76

> <JCHEM_REFRACTIVITY>
33.9645

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.86e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3-dihydroxy-3-methylvalerate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0304038 (2,3-dihydroxy-3-methylvalerate)

HMDB0304038
     RDKit          3D
2,3-dihydroxy-3-methylvalerate
 22 21  0  0  0  0  0  0  0  0999 V2000
   -1.9280    0.8483    1.0315 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5896   -0.2034   -0.0176 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1753    0.0402   -0.5672 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1205   -1.0097   -1.5925 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0205    1.3319   -1.0073 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7434   -0.2194    0.6254 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5161   -1.5378    0.9940 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1395    0.0828    0.3489 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0553   -0.7694    0.4354 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5109    1.3618   -0.0303 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5519    0.5766    2.0269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5967    1.8586    0.7350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0385    0.8760    1.1091 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3470   -0.1372   -0.7972 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6236   -1.1775    0.5132 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9991   -0.6953   -2.2096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7243   -1.1817   -2.2933 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3757   -1.9563   -1.0621 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4033    1.4027   -1.9355 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3952    0.4937    1.4245 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7833   -1.7393    1.9245 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3594    1.7543    0.3443 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
  3  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  0
  2 15  1  0
  4 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  6 20  1  0
  7 21  1  0
 10 22  1  0
M  END
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PDB for HMDB0304038 (2,3-dihydroxy-3-methylvalerate)

HEADER    PROTEIN                                 02-MAY-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-MAY-15         0                                  
HETATM    1  C   UNK     0       1.540   5.335   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.770   4.001   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.206   1.897   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.874   3.437   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       3.850   1.334   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5    6                                             
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    3    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for HMDB0304038 (2,3-dihydroxy-3-methylvalerate)

COMPND    HMDB0304038
HETATM    1  C1  UNL     1      -1.928   0.848   1.031  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.590  -0.203  -0.018  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.175   0.040  -0.567  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.121  -1.010  -1.593  1.00  0.00           C  
HETATM    5  O1  UNL     1      -0.021   1.332  -1.007  1.00  0.00           O  
HETATM    6  C5  UNL     1       0.743  -0.219   0.625  1.00  0.00           C  
HETATM    7  O2  UNL     1       0.516  -1.538   0.994  1.00  0.00           O  
HETATM    8  C6  UNL     1       2.140   0.083   0.349  1.00  0.00           C  
HETATM    9  O3  UNL     1       3.055  -0.769   0.435  1.00  0.00           O  
HETATM   10  O4  UNL     1       2.511   1.362  -0.030  1.00  0.00           O  
HETATM   11  H1  UNL     1      -1.552   0.577   2.027  1.00  0.00           H  
HETATM   12  H2  UNL     1      -1.597   1.859   0.735  1.00  0.00           H  
HETATM   13  H3  UNL     1      -3.039   0.876   1.109  1.00  0.00           H  
HETATM   14  H4  UNL     1      -2.347  -0.137  -0.797  1.00  0.00           H  
HETATM   15  H5  UNL     1      -1.624  -1.178   0.513  1.00  0.00           H  
HETATM   16  H6  UNL     1       0.999  -0.695  -2.210  1.00  0.00           H  
HETATM   17  H7  UNL     1      -0.724  -1.182  -2.293  1.00  0.00           H  
HETATM   18  H8  UNL     1       0.376  -1.956  -1.062  1.00  0.00           H  
HETATM   19  H9  UNL     1      -0.403   1.403  -1.936  1.00  0.00           H  
HETATM   20  H10 UNL     1       0.395   0.494   1.424  1.00  0.00           H  
HETATM   21  H11 UNL     1       0.783  -1.739   1.925  1.00  0.00           H  
HETATM   22  H12 UNL     1       3.359   1.754   0.344  1.00  0.00           H  
CONECT    1    2   11   12   13
CONECT    2    3   14   15
CONECT    3    4    5    6
CONECT    4   16   17   18
CONECT    5   19
CONECT    6    7    8   20
CONECT    7   21
CONECT    8    9    9   10
CONECT   10   22
END
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SMILES for HMDB0304038 (2,3-dihydroxy-3-methylvalerate)

CCC(C)(O)C(O)C(O)=O
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INCHI for HMDB0304038 (2,3-dihydroxy-3-methylvalerate)

InChI=1S/C6H12O4/c1-3-6(2,10)4(7)5(8)9/h4,7,10H,3H2,1-2H3,(H,8,9)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2,3-Dihydroxy-3-methylvalerateKegg
2,3-Dihydroxy-3-methylvaleric acidGenerator
2,3-Dihydroxy-3-methylpentanoateGenerator
Chemical FormulaC6H12O4
Average Molecular Weight148.158
Monoisotopic Molecular Weight148.073558866
IUPAC Name2,3-dihydroxy-3-methylpentanoic acid
Traditional Name2,3-dihydroxy-3-methylvalerate
CAS Registry NumberNot Available
SMILES
CCC(C)(O)C(O)C(O)=O
InChI Identifier
InChI=1S/C6H12O4/c1-3-6(2,10)4(7)5(8)9/h4,7,10H,3H2,1-2H3,(H,8,9)
InChI KeyPDGXJDXVGMHUIR-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
  • Branched fatty acid
  • Methyl-branched fatty acid
  • Short-chain hydroxy acid
  • Hydroxy fatty acid
  • Alpha-hydroxy acid
  • Hydroxy acid
  • Monosaccharide
  • Tertiary alcohol
  • 1,2-diol
  • Secondary alcohol
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Organic oxygen compound
  • Carbonyl group
  • Hydrocarbon derivative
  • Organic oxide
  • Alcohol
  • Organooxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Not AvailableNot 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 IDFDB030296
KNApSAcK IDNot Available
Chemspider ID7
KEGG Compound IDC04104
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
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 ReferencesNot Available