Showing metabocard for 2-Hydroxy-3-methylpentanoic acid (MMDBc0000340)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:35:42 UTC
Update Date2024-04-30 19:31:51 UTC
Metabolite IDMMDBc0000340
Metabolite Identification
Common Name2-Hydroxy-3-methylpentanoic acid
Description2-Hydroxy-3-methylpentanoic acid or 2-hydroxy-3-methylvaleric acid (HMVA) is an organic acid generated by L-isoleucine metabolism. It is derived from the reduction of 2-Keto-3-methylvaleric acid (KMVA), possibly through the action of a lactate dehydrogenase (PMID: 1429566 ). There are 4 stereoisomers of HMVA (2S,3S-HMVA, 2R,3R-HMVA, 2S,3R-HMVA and 2R,3S-HMVA), of which the 2S,3S and 2S,3R derivatives are generally separable. HMVA is found in the urine and blood of normal individuals but in very elevated levels in patients with maple syrup urine disease (MSUD) (PMID: 1429566 ). Maple syrup urine disease (MSUD) is an inherited metabolic disease predominantly characterized by neurological dysfunction including psychomotor/delay/mental retardation.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f91f73019f8>


  Mrv0541 02231218272D          

  9  8  0  0  1  0            999 V2000
   15.9718  -14.3316    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.4007  -13.5066    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.6863  -12.2690    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.2574  -13.0941    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.5428  -13.5066    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9718  -13.5066    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.2574  -12.2690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8283  -13.0941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6863  -13.0941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  6  0  0  0
  2  9  1  0  0  0  0
  3  9  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  4  7  1  1  0  0  0
  5  8  1  0  0  0  0
  6  9  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f91f73019f8>

HMDB0000317
     RDKit          3D
2-Hydroxy-3-methylpentanoic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
    2.3245    0.2406    0.8271 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8206    0.5497    0.7645 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2317    0.0291   -0.5178 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3857   -1.4578   -0.6647 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1375    0.5531   -0.7843 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6098    0.0124   -2.0070 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0858    0.2855    0.3000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1389   -0.3676    0.0882 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8207    0.7577    1.5752 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8955    1.0660    1.2606 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7238    0.0124   -0.1871 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5139   -0.6625    1.4414 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7223    1.6524    0.8045 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3908    0.0744    1.6717 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8815    0.4634   -1.3397 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3169   -1.7043   -1.7470 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4028   -1.7235   -0.3463 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4127   -2.0389   -0.1651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0365    1.6529   -0.9951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9410   -0.9068   -1.8826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4271    1.5120    1.9036 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  6
  4 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  6
  6 20  1  0
  9 21  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f91f73019f8>


  Mrv0541 02231218272D          

  9  8  0  0  1  0            999 V2000
   15.9718  -14.3316    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.4007  -13.5066    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.6863  -12.2690    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.2574  -13.0941    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.5428  -13.5066    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9718  -13.5066    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.2574  -12.2690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8283  -13.0941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6863  -13.0941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  6  0  0  0
  2  9  1  0  0  0  0
  3  9  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  4  7  1  1  0  0  0
  5  8  1  0  0  0  0
  6  9  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000340

> <DATABASE_NAME>
MIME

> <SMILES>
CC[C@@H](C)[C@@H](O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O3/c1-3-4(2)5(7)6(8)9/h4-5,7H,3H2,1-2H3,(H,8,9)/t4-,5-/m1/s1

> <INCHI_KEY>
RILPIWOPNGRASR-RFZPGFLSSA-N

> <FORMULA>
C6H12O3

> <MOLECULAR_WEIGHT>
132.1577

> <EXACT_MASS>
132.07864425

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
13.773780943384981

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R)-2-hydroxy-3-methylpentanoic acid

> <ALOGPS_LOGP>
0.74

> <JCHEM_LOGP>
0.8602343683333333

> <ALOGPS_LOGS>
0.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.044948135264622

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.25405925572059

> <JCHEM_PKA_STRONGEST_BASIC>
-3.8957913795351873

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
32.4364

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.49e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-hydroxy-3-methyl-valerate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007f91f73019f8>

HMDB0000317
     RDKit          3D
2-Hydroxy-3-methylpentanoic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
    2.3245    0.2406    0.8271 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8206    0.5497    0.7645 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2317    0.0291   -0.5178 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3857   -1.4578   -0.6647 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1375    0.5531   -0.7843 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6098    0.0124   -2.0070 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0858    0.2855    0.3000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1389   -0.3676    0.0882 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8207    0.7577    1.5752 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8955    1.0660    1.2606 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7238    0.0124   -0.1871 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5139   -0.6625    1.4414 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7223    1.6524    0.8045 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3908    0.0744    1.6717 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8815    0.4634   -1.3397 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3169   -1.7043   -1.7470 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4028   -1.7235   -0.3463 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4127   -2.0389   -0.1651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0365    1.6529   -0.9951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9410   -0.9068   -1.8826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4271    1.5120    1.9036 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  6
  4 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  6
  6 20  1  0
  9 21  1  0
M  END
Download

PDB for #<Metabolite:0x00007f91f73019f8>

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      29.814 -26.752   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      32.481 -25.212   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      31.148 -22.902   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      28.480 -24.442   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      27.147 -25.212   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      29.814 -25.212   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      28.480 -22.902   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      25.813 -24.442   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      31.148 -24.442   0.000  0.00  0.00           C+0
CONECT    1    6                                                            
CONECT    2    9                                                            
CONECT    3    9                                                            
CONECT    4    5    6    7                                                  
CONECT    5    4    8                                                       
CONECT    6    1    4    9                                                  
CONECT    7    4                                                            
CONECT    8    5                                                            
CONECT    9    2    3    6                                                  
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
Download

3D PDB for #<Metabolite:0x00007f91f73019f8>

COMPND    HMDB0000317
HETATM    1  C1  UNL     1       2.324   0.241   0.827  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.821   0.550   0.764  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.232   0.029  -0.518  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.386  -1.458  -0.665  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.138   0.553  -0.784  1.00  0.00           C  
HETATM    6  O1  UNL     1      -1.610   0.012  -2.007  1.00  0.00           O  
HETATM    7  C6  UNL     1      -2.086   0.285   0.300  1.00  0.00           C  
HETATM    8  O2  UNL     1      -3.139  -0.368   0.088  1.00  0.00           O  
HETATM    9  O3  UNL     1      -1.821   0.758   1.575  1.00  0.00           O  
HETATM   10  H1  UNL     1       2.895   1.066   1.261  1.00  0.00           H  
HETATM   11  H2  UNL     1       2.724   0.012  -0.187  1.00  0.00           H  
HETATM   12  H3  UNL     1       2.514  -0.662   1.441  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.722   1.652   0.805  1.00  0.00           H  
HETATM   14  H5  UNL     1       0.391   0.074   1.672  1.00  0.00           H  
HETATM   15  H6  UNL     1       0.882   0.463  -1.340  1.00  0.00           H  
HETATM   16  H7  UNL     1       0.317  -1.704  -1.747  1.00  0.00           H  
HETATM   17  H8  UNL     1       1.403  -1.723  -0.346  1.00  0.00           H  
HETATM   18  H9  UNL     1      -0.413  -2.039  -0.165  1.00  0.00           H  
HETATM   19  H10 UNL     1      -1.037   1.653  -0.995  1.00  0.00           H  
HETATM   20  H11 UNL     1      -1.941  -0.907  -1.883  1.00  0.00           H  
HETATM   21  H12 UNL     1      -2.427   1.512   1.904  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3   13   14
CONECT    3    4    5   15
CONECT    4   16   17   18
CONECT    5    6    7   19
CONECT    6   20
CONECT    7    8    8    9
CONECT    9   21
END
Download

SMILES for #<Metabolite:0x00007f91f73019f8>

CC[C@@H](C)[C@@H](O)C(O)=O
Download

INCHI for #<Metabolite:0x00007f91f73019f8>

InChI=1S/C6H12O3/c1-3-4(2)5(7)6(8)9/h4-5,7H,3H2,1-2H3,(H,8,9)/t4-,5-/m1/s1
Download
Synonyms
ValueSource
2-Hydroxy-3-methylpentanoateGenerator
(2R,3R)-2-Hydroxy-3-methyl-pentanoateHMDB
(2R,3R)-2-Hydroxy-3-methyl-pentanoic acidHMDB
(2R,3R)-2-Hydroxy-3-methylpentanoateHMDB
(2R,3R)-2-Hydroxy-3-methylpentanoic acidHMDB
2-Hydroxy-3-methyl-pentanoateHMDB
2-Hydroxy-3-methyl-pentanoic acidHMDB
2-Hydroxy-3-methyl-valerateHMDB
2-Hydroxy-3-methyl-valeric acidHMDB
2-Hydroxy-3-methylvalerateHMDB
2-Hydroxy-3-methylvaleric acidHMDB
a-Hydroxy-b-methylvalerateHMDB
a-Hydroxy-b-methylvaleric acidHMDB
alpha-Hydroxy-beta-methylvalerateHMDB
alpha-Hydroxy-beta-methylvaleric acidHMDB
HMVAHMDB
Molecular FormulaC6H12O3
Average Mass132.1577
Monoisotopic Mass132.07864425
IUPAC Name(2R,3R)-2-hydroxy-3-methylpentanoic acid
Traditional Name2-hydroxy-3-methyl-valerate
CAS Registry NumberNot Available
SMILES
CC[C@@H](C)[C@@H](O)C(O)=O
InChI Identifier
InChI=1S/C6H12O3/c1-3-4(2)5(7)6(8)9/h4-5,7H,3H2,1-2H3,(H,8,9)/t4-,5-/m1/s1
InChI KeyRILPIWOPNGRASR-RFZPGFLSSA-N