Showing metabocard for 3-Carboxy-2-hydroxy-4-methylpentanoate (MMDBc0049884)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-04-29 22:45:31 UTC
Update Date2022-09-01 02:16:52 UTC
Metabolite IDMMDBc0049884
Metabolite Identification
Common Name3-Carboxy-2-hydroxy-4-methylpentanoate
Description3-Carboxy-2-hydroxy-4-methylpentanoate (CAS: 16048-89-8), also known as 3-isopropylmalic acid, is an intermediate in valine, leucine, and isoleucine biosynthesis. It is a substrate for 3-isopropylmalate dehydrogenase (TT_C0867) and can be generated from the reduction of 2-isopropyl-3-oxosuccinate. Leucine biosynthesis involves a five-step conversion process starting with the valine precursor 2-keto-isovalerate. The final step in this pathway is catalyzed by two transaminases of broad specificity: branched-chain amino acid transferase (IlvE) and tyrosine aminotransferase (TyrB). This pathway is part of the super pathway of leucine, valine, and isoleucine biosynthesis that generates not only isoleucine and valine but also leucine.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f923dd35ac8>


  Mrv1652309042000342D          

 12 11  0  0  1  0            999 V2000
    0.3562    0.0001    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3562   -0.4092    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0687   -0.4092    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3562    0.8263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0725    0.0001    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3562   -1.2356    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7851    0.0001    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0687   -1.2356    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0725    1.2356    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3600    1.2356    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0914    0.8983    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7851   -0.4130    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
  2  5  1  0  0  0  0
  2  6  1  1  0  0  0
  5 11  2  0  0  0  0
  5 12  1  0  0  0  0
  3  8  2  0  0  0  0
  3  7  1  0  0  0  0
  4 10  1  0  0  0  0
  4  9  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f923dd35ac8>

HMDB0012156
     RDKit          3D
3-Isopropylmalic acid
 24 23  0  0  0  0  0  0  0  0999 V2000
   -1.5392    0.3182   -1.2008 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9392   -0.6098   -0.2063 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0591   -1.0032    0.7681 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1802   -0.0398    0.6024 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1708    1.1255    1.4035 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0347    1.0636    2.6504 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6526    2.3230    0.8952 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3767    0.3669   -0.2519 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3086    0.8721    0.6687 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9989   -0.7480   -0.9670 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3675   -1.3561   -1.8555 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2837   -1.1385   -0.6694 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2886    0.9981   -0.7051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1405   -0.2863   -1.9185 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8043    0.8759   -1.8053 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6468   -1.5467   -0.7138 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0367   -2.0852    0.9776 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0515   -0.7777    0.3387 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9580   -0.3893    1.6800 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5520   -0.8416    1.2676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3369    2.7694    0.0665 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1231    1.2221   -0.9120 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5126    0.1398    1.3062 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9557   -1.2523   -1.4194 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  4  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  2  0
 10 12  1  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  2 16  1  0
  3 17  1  0
  3 18  1  0
  3 19  1  0
  4 20  1  1
  7 21  1  0
  8 22  1  6
  9 23  1  0
 12 24  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f923dd35ac8>


  Mrv1652309042000342D          

 12 11  0  0  1  0            999 V2000
    0.3562    0.0001    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3562   -0.4092    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0687   -0.4092    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3562    0.8263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0725    0.0001    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3562   -1.2356    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7851    0.0001    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0687   -1.2356    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0725    1.2356    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3600    1.2356    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0914    0.8983    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7851   -0.4130    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
  2  5  1  0  0  0  0
  2  6  1  1  0  0  0
  5 11  2  0  0  0  0
  5 12  1  0  0  0  0
  3  8  2  0  0  0  0
  3  7  1  0  0  0  0
  4 10  1  0  0  0  0
  4  9  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0049884

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C7H12O5/c1-3(2)4(6(9)10)5(8)7(11)12/h3-5,8H,1-2H3,(H,9,10)(H,11,12)/t4-,5+/m0/s1

> <INCHI_KEY>
RNQHMTFBUSSBJQ-CRCLSJGQSA-N

> <FORMULA>
C7H12O5

> <MOLECULAR_WEIGHT>
176.1672

> <EXACT_MASS>
176.068473494

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
16.470268701415307

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S)-2-hydroxy-3-(propan-2-yl)butanedioic acid

> <ALOGPS_LOGP>
0.28

> <JCHEM_LOGP>
0.1609326116666665

> <ALOGPS_LOGS>
-0.33

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.519667331107795

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.6770578154838125

> <JCHEM_PKA_STRONGEST_BASIC>
-4.015599488752675

> <JCHEM_POLAR_SURFACE_AREA>
94.83000000000001

> <JCHEM_REFRACTIVITY>
38.5993

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.33e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S)-3-isopropylmalic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007f923dd35ac8>

HMDB0012156
     RDKit          3D
3-Isopropylmalic acid
 24 23  0  0  0  0  0  0  0  0999 V2000
   -1.5392    0.3182   -1.2008 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9392   -0.6098   -0.2063 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0591   -1.0032    0.7681 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1802   -0.0398    0.6024 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1708    1.1255    1.4035 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0347    1.0636    2.6504 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6526    2.3230    0.8952 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3767    0.3669   -0.2519 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3086    0.8721    0.6687 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9989   -0.7480   -0.9670 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3675   -1.3561   -1.8555 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2837   -1.1385   -0.6694 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2886    0.9981   -0.7051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1405   -0.2863   -1.9185 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8043    0.8759   -1.8053 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6468   -1.5467   -0.7138 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0367   -2.0852    0.9776 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0515   -0.7777    0.3387 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9580   -0.3893    1.6800 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5520   -0.8416    1.2676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3369    2.7694    0.0665 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1231    1.2221   -0.9120 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5126    0.1398    1.3062 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9557   -1.2523   -1.4194 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  4  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  2  0
 10 12  1  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  2 16  1  0
  3 17  1  0
  3 18  1  0
  3 19  1  0
  4 20  1  1
  7 21  1  0
  8 22  1  6
  9 23  1  0
 12 24  1  0
M  END
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PDB for #<Metabolite:0x00007f923dd35ac8>

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       0.665   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.665  -0.764   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.995  -0.764   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.665   1.542   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.002   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -0.665  -2.306   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       3.332   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       1.995  -2.306   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       2.002   2.306   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.672   2.306   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -2.037   1.677   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -3.332  -0.771   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    8    7                                                  
CONECT    4    1   10    9                                                  
CONECT    5    2   11   12                                                  
CONECT    6    2                                                            
CONECT    7    3                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    4                                                            
CONECT   11    5                                                            
CONECT   12    5                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END
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3D PDB for #<Metabolite:0x00007f923dd35ac8>

COMPND    HMDB0012156
HETATM    1  C1  UNL     1      -1.539   0.318  -1.201  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.939  -0.610  -0.206  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.059  -1.003   0.768  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.180  -0.040   0.602  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.171   1.126   1.403  1.00  0.00           C  
HETATM    6  O1  UNL     1      -0.035   1.064   2.650  1.00  0.00           O  
HETATM    7  O2  UNL     1      -0.653   2.323   0.895  1.00  0.00           O  
HETATM    8  C6  UNL     1       1.377   0.367  -0.252  1.00  0.00           C  
HETATM    9  O3  UNL     1       2.309   0.872   0.669  1.00  0.00           O  
HETATM   10  C7  UNL     1       1.999  -0.748  -0.967  1.00  0.00           C  
HETATM   11  O4  UNL     1       1.368  -1.356  -1.856  1.00  0.00           O  
HETATM   12  O5  UNL     1       3.284  -1.138  -0.669  1.00  0.00           O  
HETATM   13  H1  UNL     1      -2.289   0.998  -0.705  1.00  0.00           H  
HETATM   14  H2  UNL     1      -2.141  -0.286  -1.918  1.00  0.00           H  
HETATM   15  H3  UNL     1      -0.804   0.876  -1.805  1.00  0.00           H  
HETATM   16  H4  UNL     1      -0.647  -1.547  -0.714  1.00  0.00           H  
HETATM   17  H5  UNL     1      -2.037  -2.085   0.978  1.00  0.00           H  
HETATM   18  H6  UNL     1      -3.051  -0.778   0.339  1.00  0.00           H  
HETATM   19  H7  UNL     1      -1.958  -0.389   1.680  1.00  0.00           H  
HETATM   20  H8  UNL     1       0.552  -0.842   1.268  1.00  0.00           H  
HETATM   21  H9  UNL     1      -0.337   2.769   0.067  1.00  0.00           H  
HETATM   22  H10 UNL     1       1.123   1.222  -0.912  1.00  0.00           H  
HETATM   23  H11 UNL     1       2.513   0.140   1.306  1.00  0.00           H  
HETATM   24  H12 UNL     1       3.956  -1.252  -1.419  1.00  0.00           H  
CONECT    1    2   13   14   15
CONECT    2    3    4   16
CONECT    3   17   18   19
CONECT    4    5    8   20
CONECT    5    6    6    7
CONECT    7   21
CONECT    8    9   10   22
CONECT    9   23
CONECT   10   11   11   12
CONECT   12   24
END
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SMILES for #<Metabolite:0x00007f923dd35ac8>

CC(C)[C@@H]([C@@H](O)C(O)=O)C(O)=O
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INCHI for #<Metabolite:0x00007f923dd35ac8>

InChI=1S/C7H12O5/c1-3(2)4(6(9)10)5(8)7(11)12/h3-5,8H,1-2H3,(H,9,10)(H,11,12)/t4-,5+/m0/s1
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Synonyms
ValueSource
(2R,3S)-2-Hydroxy-3-isopropylsuccinic acidChEBI
(2R,3S)-3-Carboxy-2-hydroxy-4-methylpentanoic acidChEBI
2-D-Threo-hydroxy-3-carboxy-isocaproateChEBI
2-D-Threo-hydroxy-3-carboxyisocaproic acidChEBI
3-Carboxy-2-hydroxy-4-methylpentanoateChEBI
3-IsopropylmalateChEBI
(2R,3S)-2-Hydroxy-3-isopropylsuccinateGenerator
(2R,3S)-3-Carboxy-2-hydroxy-4-methylpentanoateGenerator
2-D-Threo-hydroxy-3-carboxy-isocaproic acidGenerator
2-D-Threo-hydroxy-3-carboxyisocaproateGenerator
3-Carboxy-2-hydroxy-4-methylpentanoic acidGenerator
3-Isopropylmalic acidGenerator
(2R,3S)-2-Hydroxy-3-(propan-2-yl)butanedioateHMDB
(2R,3S)-2-Hydroxy-3-(propan-2-yl)butanedioic acidHMDB
(2R,3S)-3-IsopropylmalateHMDB
(2R,3S)-3-Isopropylmalic acidHMDB
3-3-Isopropylmalic acidHMDB
IPMHMDB
beta-Isopropylmalate, erythro-(L)-isomerMeSH, HMDB
beta-IsopropylmalateMeSH, HMDB
(2R,3S)-2-Hydroxy-3-(1-methylethyl)butanedioic acidHMDB
2-Hydroxy-3-(1-methylethyl)butanedioic acidHMDB
IsopropylmalateHMDB
Isopropylmalic acidHMDB
beta-Isopropylmalic acidHMDB
β-Isopropylmalic acidHMDB
Molecular FormulaC7H12O5
Average Mass176.1672
Monoisotopic Mass176.068473494
IUPAC Name(2R,3S)-2-hydroxy-3-(propan-2-yl)butanedioic acid
Traditional Name(2R,3S)-3-isopropylmalic acid
CAS Registry NumberNot Available
SMILES
CC(C)[C@@H]([C@@H](O)C(O)=O)C(O)=O
InChI Identifier
InChI=1S/C7H12O5/c1-3(2)4(6(9)10)5(8)7(11)12/h3-5,8H,1-2H3,(H,9,10)(H,11,12)/t4-,5+/m0/s1
InChI KeyRNQHMTFBUSSBJQ-CRCLSJGQSA-N