Showing metabocard for 3-Methylglutaric acid (MMDBc0000815)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 22:03:39 UTC
Update Date2024-04-30 19:33:45 UTC
Metabolite IDMMDBc0000815
Metabolite Identification
Common Name3-Methylglutaric acid
DescriptionMethylglutaric acid is a leucine metabolite. A large amount of methylglutaric acid is identified in urine of patients with deficiency of 3-methylglutaconyl coenzyme A hydratase (PMID 6181239 ). Methylglutaric acid is also found to be associated with 3-hydroxy-3-methylglutaryl-CoA lyase deficiency, another inborn error of metabolism.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00005645c9fdca90>


  Mrv1652305271900212D          

 10  9  0  0  0  0            999 V2000
   21.4256  -11.6931    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1387  -11.6931    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.7112  -12.9306    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.8532  -12.9306    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.2822  -12.1056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.9966  -11.6931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5677  -11.6931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.2822  -12.9306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.7112  -12.1056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8532  -12.1056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  2 10  1  0  0  0  0
  3  9  2  0  0  0  0
  4 10  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  5  8  1  0  0  0  0
  6  9  1  0  0  0  0
  7 10  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00005645c9fdca90>

HMDB0000752
     RDKit          3D
Methylglutaric acid
 20 19  0  0  0  0  0  0  0  0999 V2000
   -0.6223   -1.4416   -0.6775 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0892   -0.1330   -0.3023 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3684   -0.5178    0.3509 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2161    0.5864    0.7943 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9607    1.8111    0.6689 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4215    0.2826    1.4145 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8199    0.6810    0.5874 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1003    1.0134   -0.0942 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1534    1.9473   -0.9477 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2884    0.3334    0.1577 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6978   -1.3202   -0.7754 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1093   -1.8416   -1.5711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4437   -2.1216    0.2066 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2444    0.4326   -1.2444 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9613   -1.0940   -0.4147 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1554   -1.2601    1.1540 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2412    0.8664    1.3406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3350    1.5669    0.9963 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1005    0.0420    1.4635 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9876    0.1669   -0.5574 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
  4  5  2  0
  4  6  1  0
  2  7  1  0
  7  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
  3 15  1  0
  3 16  1  0
  6 17  1  0
  7 18  1  0
  7 19  1  0
 10 20  1  0
M  END
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3D SDF for #<Metabolite:0x00005645c9fdca90>


  Mrv1652305271900212D          

 10  9  0  0  0  0            999 V2000
   21.4256  -11.6931    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1387  -11.6931    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.7112  -12.9306    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.8532  -12.9306    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.2822  -12.1056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.9966  -11.6931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5677  -11.6931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.2822  -12.9306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.7112  -12.1056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8532  -12.1056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  2 10  1  0  0  0  0
  3  9  2  0  0  0  0
  4 10  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  5  8  1  0  0  0  0
  6  9  1  0  0  0  0
  7 10  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000815

> <DATABASE_NAME>
MIME

> <SMILES>
CC(CC(O)=O)CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O4/c1-4(2-5(7)8)3-6(9)10/h4H,2-3H2,1H3,(H,7,8)(H,9,10)

> <INCHI_KEY>
XJMMNTGIMDZPMU-UHFFFAOYSA-N

> <FORMULA>
C6H10O4

> <MOLECULAR_WEIGHT>
146.1412

> <EXACT_MASS>
146.057908808

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.87828651210858

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-methylpentanedioic acid

> <ALOGPS_LOGP>
0.33

> <JCHEM_LOGP>
0.3331047939999997

> <ALOGPS_LOGS>
-0.60

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.694332576440712

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.9135664414162874

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
32.6866

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.69e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methylglutaric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00005645c9fdca90>

HMDB0000752
     RDKit          3D
Methylglutaric acid
 20 19  0  0  0  0  0  0  0  0999 V2000
   -0.6223   -1.4416   -0.6775 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0892   -0.1330   -0.3023 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3684   -0.5178    0.3509 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2161    0.5864    0.7943 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9607    1.8111    0.6689 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4215    0.2826    1.4145 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8199    0.6810    0.5874 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1003    1.0134   -0.0942 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1534    1.9473   -0.9477 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2884    0.3334    0.1577 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6978   -1.3202   -0.7754 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1093   -1.8416   -1.5711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4437   -2.1216    0.2066 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2444    0.4326   -1.2444 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9613   -1.0940   -0.4147 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1554   -1.2601    1.1540 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2412    0.8664    1.3406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3350    1.5669    0.9963 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1005    0.0420    1.4635 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9876    0.1669   -0.5574 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
  4  5  2  0
  4  6  1  0
  2  7  1  0
  7  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
  3 15  1  0
  3 16  1  0
  6 17  1  0
  7 18  1  0
  7 19  1  0
 10 20  1  0
M  END
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PDB for #<Metabolite:0x00005645c9fdca90>

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  O   UNK     0      39.994 -21.827   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      31.992 -21.827   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      38.661 -24.137   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      33.326 -24.137   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      35.993 -22.597   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      37.327 -21.827   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      34.660 -21.827   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      35.993 -24.137   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      38.661 -22.597   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      33.326 -22.597   0.000  0.00  0.00           C+0
CONECT    1    9                                                            
CONECT    2   10                                                            
CONECT    3    9                                                            
CONECT    4   10                                                            
CONECT    5    6    7    8                                                  
CONECT    6    5    9                                                       
CONECT    7    5   10                                                       
CONECT    8    5                                                            
CONECT    9    1    3    6                                                  
CONECT   10    2    4    7                                                  
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for #<Metabolite:0x00005645c9fdca90>

COMPND    HMDB0000752
HETATM    1  C1  UNL     1      -0.622  -1.442  -0.678  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.089  -0.133  -0.302  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.368  -0.518   0.351  1.00  0.00           C  
HETATM    4  C4  UNL     1       2.216   0.586   0.794  1.00  0.00           C  
HETATM    5  O1  UNL     1       1.961   1.811   0.669  1.00  0.00           O  
HETATM    6  O2  UNL     1       3.421   0.283   1.415  1.00  0.00           O  
HETATM    7  C5  UNL     1      -0.820   0.681   0.587  1.00  0.00           C  
HETATM    8  C6  UNL     1      -2.100   1.013  -0.094  1.00  0.00           C  
HETATM    9  O3  UNL     1      -2.153   1.947  -0.948  1.00  0.00           O  
HETATM   10  O4  UNL     1      -3.288   0.333   0.158  1.00  0.00           O  
HETATM   11  H1  UNL     1      -1.698  -1.320  -0.775  1.00  0.00           H  
HETATM   12  H2  UNL     1      -0.109  -1.842  -1.571  1.00  0.00           H  
HETATM   13  H3  UNL     1      -0.444  -2.122   0.207  1.00  0.00           H  
HETATM   14  H4  UNL     1       0.244   0.433  -1.244  1.00  0.00           H  
HETATM   15  H5  UNL     1       1.961  -1.094  -0.415  1.00  0.00           H  
HETATM   16  H6  UNL     1       1.155  -1.260   1.154  1.00  0.00           H  
HETATM   17  H7  UNL     1       4.241   0.866   1.341  1.00  0.00           H  
HETATM   18  H8  UNL     1      -0.335   1.567   0.996  1.00  0.00           H  
HETATM   19  H9  UNL     1      -1.100   0.042   1.463  1.00  0.00           H  
HETATM   20  H10 UNL     1      -3.988   0.167  -0.557  1.00  0.00           H  
CONECT    1    2   11   12   13
CONECT    2    3    7   14
CONECT    3    4   15   16
CONECT    4    5    5    6
CONECT    6   17
CONECT    7    8   18   19
CONECT    8    9    9   10
CONECT   10   20
END
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SMILES for #<Metabolite:0x00005645c9fdca90>

CC(CC(O)=O)CC(O)=O
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INCHI for #<Metabolite:0x00005645c9fdca90>

InChI=1S/C6H10O4/c1-4(2-5(7)8)3-6(9)10/h4H,2-3H2,1H3,(H,7,8)(H,9,10)
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Synonyms
ValueSource
beta-Methylglutaric acidChEBI
b-MethylglutarateGenerator
b-Methylglutaric acidGenerator
beta-MethylglutarateGenerator
Β-methylglutarateGenerator
Β-methylglutaric acidGenerator
MethylglutarateGenerator
3-Methyl-glutarateHMDB
3-Methyl-glutaric acidHMDB
3-MethylglutarateHMDB
3-Methylglutaric acidHMDB
3-MethylpentanedioateHMDB
3-Methylpentanedioic acidHMDB
b-Methyl-glutaric acidHMDB
beta-Methyl-glutaric acidHMDB
Molecular FormulaC6H10O4
Average Mass146.1412
Monoisotopic Mass146.057908808
IUPAC Name3-methylpentanedioic acid
Traditional Namemethylglutaric acid
CAS Registry NumberNot Available
SMILES
CC(CC(O)=O)CC(O)=O
InChI Identifier
InChI=1S/C6H10O4/c1-4(2-5(7)8)3-6(9)10/h4H,2-3H2,1H3,(H,7,8)(H,9,10)
InChI KeyXJMMNTGIMDZPMU-UHFFFAOYSA-N