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Showing metabocard for (R)-2,3-Dihydroxy-3-methylvalerate (HMDB0012140)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2009-04-06 16:19:53 UTC
Update Date2023-02-21 17:17:39 UTC
HMDB IDHMDB0012140
Secondary Accession Numbers
  • HMDB12140
Metabolite Identification
Common Name(R)-2,3-Dihydroxy-3-methylvalerate
Description(R)-2,3-Dihydroxy-methylvalerate is an intermediate in valine, leucine, and isoleucine biosynthesis. The pathway of valine biosynthesis is a four-step pathway that shares all of its steps with the parallel pathway of isoleucine biosynthesis. These entwined pathways are part of the superpathway of leucine, valine, and isoleucine biosynthesis, which generates not only isoleucine and valine but also leucine. (R)-2,3-Dihydroxy-methylvalerate is generated from 3-hydroxy-3-methyl-2-oxopentanoic acid via the enzyme ketol-acid reductoisomerase (EC 1.1.1.86). It is converted into (S)-3-methyl-2-oxopentanoic via the dihydroxy-acid dehydratase (EC 4.2.1.9).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0012140 ((R)-2,3-Dihydroxy-3-methylvalerate)

  Mrv1652309042000342D          

 10  9  0  0  1  0            999 V2000
   15.4113  -13.3962    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.1244  -13.8112    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.6949  -13.8112    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8150  -12.6836    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9967  -12.6836    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8407  -13.3962    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1206  -14.7118    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.9860  -13.4038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5462  -13.8112    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8370  -12.5703    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  6  0  0  0
  1  5  1  1  0  0  0
  2  6  1  0  0  0  0
  2  7  1  6  0  0  0
  3  8  1  0  0  0  0
  6  9  1  0  0  0  0
  6 10  2  0  0  0  0
M  END
Download

3D MOL for HMDB0012140 ((R)-2,3-Dihydroxy-3-methylvalerate)

HMDB0012140
     RDKit          3D
(R)-2,3-Dihydroxy-3-methylvalerate
 22 21  0  0  0  0  0  0  0  0999 V2000
   -2.2884    0.5495    0.2894 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8048    0.6478    0.5794 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0785   -0.3710   -0.2662 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6332   -1.7409    0.1310 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2911   -0.1214   -1.6108 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3986   -0.4143    0.0219 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9202   -1.4577   -0.7725 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1101    0.8216   -0.3666 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0012    0.8609   -1.2524 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7972    2.0157    0.2643 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6067    1.3367   -0.4491 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5824   -0.4279   -0.1302 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8672    0.6931    1.2281 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6281    0.3612    1.6497 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5117    1.6878    0.3640 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1734   -2.5134    0.0653 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4430   -2.0697   -0.5370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9113   -1.6879    1.1959 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3959    0.8710   -1.7065 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6062   -0.6796    1.0711 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6721   -1.2133   -1.7034 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3633    2.8517    0.1824 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  6
  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  1
  7 21  1  0
 10 22  1  0
M  END
Download

3D SDF for HMDB0012140 ((R)-2,3-Dihydroxy-3-methylvalerate)

  Mrv1652309042000342D          

 10  9  0  0  1  0            999 V2000
   15.4113  -13.3962    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.1244  -13.8112    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.6949  -13.8112    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8150  -12.6836    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9967  -12.6836    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8407  -13.3962    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1206  -14.7118    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.9860  -13.4038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5462  -13.8112    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8370  -12.5703    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  6  0  0  0
  1  5  1  1  0  0  0
  2  6  1  0  0  0  0
  2  7  1  6  0  0  0
  3  8  1  0  0  0  0
  6  9  1  0  0  0  0
  6 10  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0012140

> <DATABASE_NAME>
hmdb

> <SMILES>
CC[C@@](C)(O)[C@@H](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)/t4-,6+/m0/s1

> <INCHI_KEY>
PDGXJDXVGMHUIR-UJURSFKZSA-N

> <FORMULA>
C6H12O4

> <MOLECULAR_WEIGHT>
148.1571

> <EXACT_MASS>
148.073558872

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
14.433750785635485

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R)-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>
77.75999999999999

> <JCHEM_REFRACTIVITY>
33.9645

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.86e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R)-2,3-dihydroxy-3-methylpentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0012140 ((R)-2,3-Dihydroxy-3-methylvalerate)

HMDB0012140
     RDKit          3D
(R)-2,3-Dihydroxy-3-methylvalerate
 22 21  0  0  0  0  0  0  0  0999 V2000
   -2.2884    0.5495    0.2894 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8048    0.6478    0.5794 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0785   -0.3710   -0.2662 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6332   -1.7409    0.1310 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2911   -0.1214   -1.6108 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3986   -0.4143    0.0219 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9202   -1.4577   -0.7725 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1101    0.8216   -0.3666 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0012    0.8609   -1.2524 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7972    2.0157    0.2643 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6067    1.3367   -0.4491 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5824   -0.4279   -0.1302 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8672    0.6931    1.2281 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6281    0.3612    1.6497 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5117    1.6878    0.3640 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1734   -2.5134    0.0653 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4430   -2.0697   -0.5370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9113   -1.6879    1.1959 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3959    0.8710   -1.7065 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6062   -0.6796    1.0711 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6721   -1.2133   -1.7034 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3633    2.8517    0.1824 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  6
  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  1
  7 21  1  0
 10 22  1  0
M  END
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PDB for HMDB0012140 ((R)-2,3-Dihydroxy-3-methylvalerate)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0      28.768 -25.006   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      30.099 -25.781   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      27.430 -25.781   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      29.521 -23.676   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      27.994 -23.676   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      31.436 -25.006   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      30.092 -27.462   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      26.107 -25.020   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      32.753 -25.781   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      31.429 -23.465   0.000  0.00  0.00           O+0
CONECT    1    2    3    4    5                                             
CONECT    2    1    6    7                                                  
CONECT    3    1    8                                                       
CONECT    4    1                                                            
CONECT    5    1                                                            
CONECT    6    2    9   10                                                  
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    6                                                            
CONECT   10    6                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for HMDB0012140 ((R)-2,3-Dihydroxy-3-methylvalerate)

COMPND    HMDB0012140
HETATM    1  C1  UNL     1      -2.288   0.550   0.289  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.805   0.648   0.579  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.078  -0.371  -0.266  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.633  -1.741   0.131  1.00  0.00           C  
HETATM    5  O1  UNL     1      -0.291  -0.121  -1.611  1.00  0.00           O  
HETATM    6  C5  UNL     1       1.399  -0.414   0.022  1.00  0.00           C  
HETATM    7  O2  UNL     1       1.920  -1.458  -0.772  1.00  0.00           O  
HETATM    8  C6  UNL     1       2.110   0.822  -0.367  1.00  0.00           C  
HETATM    9  O3  UNL     1       3.001   0.861  -1.252  1.00  0.00           O  
HETATM   10  O4  UNL     1       1.797   2.016   0.264  1.00  0.00           O  
HETATM   11  H1  UNL     1      -2.607   1.337  -0.449  1.00  0.00           H  
HETATM   12  H2  UNL     1      -2.582  -0.428  -0.130  1.00  0.00           H  
HETATM   13  H3  UNL     1      -2.867   0.693   1.228  1.00  0.00           H  
HETATM   14  H4  UNL     1      -0.628   0.361   1.650  1.00  0.00           H  
HETATM   15  H5  UNL     1      -0.512   1.688   0.364  1.00  0.00           H  
HETATM   16  H6  UNL     1       0.173  -2.513   0.065  1.00  0.00           H  
HETATM   17  H7  UNL     1      -1.443  -2.070  -0.537  1.00  0.00           H  
HETATM   18  H8  UNL     1      -0.911  -1.688   1.196  1.00  0.00           H  
HETATM   19  H9  UNL     1      -0.396   0.871  -1.706  1.00  0.00           H  
HETATM   20  H10 UNL     1       1.606  -0.680   1.071  1.00  0.00           H  
HETATM   21  H11 UNL     1       1.672  -1.213  -1.703  1.00  0.00           H  
HETATM   22  H12 UNL     1       2.363   2.852   0.182  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 HMDB0012140 ((R)-2,3-Dihydroxy-3-methylvalerate)

CC[C@@](C)(O)[C@@H](O)C(O)=O
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INCHI for HMDB0012140 ((R)-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)/t4-,6+/m0/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC6H12O4
Average Molecular Weight148.1571
Monoisotopic Molecular Weight148.073558872
IUPAC Name(2R,3R)-2,3-dihydroxy-3-methylpentanoic acid
Traditional Name(2R,3R)-2,3-dihydroxy-3-methylpentanoic acid
CAS Registry Number562-43-6
SMILES
CC[C@@](C)(O)[C@@H](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)/t4-,6+/m0/s1
InChI KeyPDGXJDXVGMHUIR-UJURSFKZSA-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
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
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 LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB03675
Phenol Explorer Compound IDNot Available
FooDB IDFDB028798
KNApSAcK IDNot Available
Chemspider ID395044
KEGG Compound IDC06007
BioCyc ID1-KETO-2-METHYLVALERATE
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound448154
PDB IDDMV
ChEBI ID27512
Food Biomarker OntologyNot Available
VMH ID23DHMP
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  2. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  3. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  4. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  5. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.