Showing metabocard for (R)-2,3-Dihydroxy-3-methylpentanoate (MMDBc0049902)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-04-29 22:45:52 UTC
Update Date2022-09-01 02:17:07 UTC
Metabolite IDMMDBc0049902
Metabolite Identification
Common Name(R)-2,3-Dihydroxy-3-methylpentanoate
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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000556b6afb7338>


  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
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3D MOL for #<Metabolite:0x0000556b6afb7338>

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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3D SDF for #<Metabolite:0x0000556b6afb7338>


  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>
MMDBc0049902

> <DATABASE_NAME>
MIME

> <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

$$$$
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3D-SDF for #<Metabolite:0x0000556b6afb7338>

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 #<Metabolite:0x0000556b6afb7338>

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 #<Metabolite:0x0000556b6afb7338>

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 #<Metabolite:0x0000556b6afb7338>

CC[C@@](C)(O)[C@@H](O)C(O)=O
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INCHI for #<Metabolite:0x0000556b6afb7338>

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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Synonyms
ValueSource
(2R,3R)-2,3-Dihydroxy-3-methylvaleric acidChEBI
(2R,3R)-2,3-Dihydroxy-3-methylpentanoateKegg
(2R,3R)-2,3-Dihydroxy-3-methylvalerateGenerator
(2R,3R)-2,3-Dihydroxy-3-methylpentanoic acidGenerator
(R)-2,3-Dihydroxy-3-methylvaleric acidGenerator
(R) 2,3-Dihydroxy-3-methylvaleric acidGenerator, HMDB
(R)-2,3-Dihydroxy-3-methylpentanoateHMDB
(R)-2,3-Dihydroxy-3-methylpentanoic acidHMDB
(R)-2,3-Dihydroxy-3-methylvalerateHMDB, KEGG
1-keto-2-MethylvalerateHMDB
2,3-Dihydroxy-3-methyl-valeric acidHMDB
2,3-Dihydroxy-3-methylpentanoateHMDB
2,3-Dihydroxy-3-methylpentanoic acidHMDB
2,3-Dihydroxy-valerianic acidHMDB
4,5-Dideoxy-3-C-methyl-pentonic acidHMDB
alpha,beta-Dihydroxy-beta-methylvaleric acidHMDB
CID8HMDB
DMVHMDB
Molecular FormulaC6H12O4
Average Mass148.1571
Monoisotopic Mass148.073558872
IUPAC Name(2R,3R)-2,3-dihydroxy-3-methylpentanoic acid
Traditional Name(2R,3R)-2,3-dihydroxy-3-methylpentanoic acid
CAS Registry NumberNot Available
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