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Showing metabocard for 3-Isopropylmalic acid (HMDB0012156)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2009-04-06 16:20:09 UTC
Update Date2023-02-21 17:17:41 UTC
HMDB IDHMDB0012156
Secondary Accession Numbers
  • HMDB12156
Metabolite Identification
Common Name3-Isopropylmalic acid
Description3-Isopropylmalic acid (CAS: 16048-89-8) 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0012156 (3-Isopropylmalic acid)

  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 HMDB0012156 (3-Isopropylmalic acid)

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 HMDB0012156 (3-Isopropylmalic acid)

  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>
HMDB0012156

> <DATABASE_NAME>
hmdb

> <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 HMDB0012156 (3-Isopropylmalic acid)

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

PDB for HMDB0012156 (3-Isopropylmalic acid)

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 HMDB0012156 (3-Isopropylmalic acid)

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 HMDB0012156 (3-Isopropylmalic acid)

CC(C)[C@@H]([C@@H](O)C(O)=O)C(O)=O
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INCHI for HMDB0012156 (3-Isopropylmalic acid)

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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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC7H12O5
Average Molecular Weight176.1672
Monoisotopic Molecular Weight176.068473494
IUPAC Name(2R,3S)-2-hydroxy-3-(propan-2-yl)butanedioic acid
Traditional Name(2R,3S)-3-isopropylmalic acid
CAS Registry Number126576-14-5
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
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
  • Beta-hydroxy acid
  • Branched fatty acid
  • Hydroxy fatty acid
  • Short-chain hydroxy acid
  • Methyl-branched fatty acid
  • Alpha-hydroxy acid
  • Hydroxy acid
  • Dicarboxylic acid or derivatives
  • Secondary alcohol
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Organic oxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Not Available127.46http://allccs.zhulab.cn/database/detail?ID=AllCCS00000279
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 IDFDB028813
KNApSAcK IDC00019691
Chemspider ID4575349
KEGG Compound IDC04411
BioCyc ID2-D-THREO-HYDROXY-3-CARBOXY-ISOCAPROATE
BiGG IDNot Available
Wikipedia LinkIsopropylmalic acid
METLIN IDNot Available
PubChem Compound5462261
PDB IDIPM
ChEBI ID43468
Food Biomarker OntologyNot Available
VMH ID3C2HMP
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.