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Showing NP-Card for 2-Methylglutaric acid (NP0001469)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2024-09-17 15:45:20 UTC
NP-MRD IDNP0001469
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-Methylglutaric acid
Description2-Methylglutaric acid, also known as alpha-methylglutarate or 2-methylpentanedioate, belongs to the class of organic compounds known as methyl-branched fatty acids. These are fatty acids with an acyl chain that has a methyl branch. Usually, they are saturated and contain only one or more methyl group. However, branches other than methyl may be present. 2-Methylglutaric acid is also classified as an alpha,omega-dicarboxylic acid. It is glutaric acid substituted at position 2 by a methyl group. 2-Methylglutaric acid arises from the microbial metabolism of the isoprenoid alkaloid pristane (PMID: 4327007 ; PMID: 20143352 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0001469 (2-Methylglutaric acid)


  Mrv1652305261923542D          

 10  9  0  0  0  0            999 V2000
   10.9938   -9.4604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.2793   -8.2229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7068   -9.4604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4214   -8.2229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.5648   -9.4604    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8503   -9.0479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1358   -9.4604    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5648  -10.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2793   -9.0479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4214   -9.0479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  2  9  2  0  0  0  0
  3 10  1  0  0  0  0
  4 10  2  0  0  0  0
  5  6  1  0  0  0  0
  5  8  1  0  0  0  0
  5  9  1  0  0  0  0
  6  7  1  0  0  0  0
  7 10  1  0  0  0  0
M  END
Download

3D MOL for NP0001469 (2-Methylglutaric acid)

HMDB0000422
     RDKit          3D
2-Methylglutaric acid
 20 19  0  0  0  0  0  0  0  0999 V2000
   -1.2582   -1.4926   -0.6851 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1097   -0.2330    0.0961 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1451    0.5332   -0.2306 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3773   -0.2946    0.0522 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5884    0.4956   -0.2825 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4746    1.6732   -0.7291 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8675    0.0081   -0.1309 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2783    0.6224   -0.0998 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2057    0.2250   -0.8500 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4505    1.8662    0.4891 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5733   -2.2751   -0.3041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1433   -1.2959   -1.7693 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3232   -1.8369   -0.5611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0575   -0.4779    1.1952 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1617    1.4189    0.4449 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1706    0.8615   -1.2727 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2933   -1.2211   -0.5450 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3896   -0.5453    1.1197 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1145   -0.7656    0.4711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1826    2.7338    0.0269 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  1  0
  5  6  2  0
  5  7  1  0
  2  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
  4 17  1  0
  4 18  1  0
  7 19  1  0
 10 20  1  0
M  END
Download

3D SDF for NP0001469 (2-Methylglutaric acid)


  Mrv1652305261923542D          

 10  9  0  0  0  0            999 V2000
   10.9938   -9.4604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.2793   -8.2229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7068   -9.4604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4214   -8.2229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.5648   -9.4604    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8503   -9.0479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1358   -9.4604    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5648  -10.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2793   -9.0479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4214   -9.0479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  2  9  2  0  0  0  0
  3 10  1  0  0  0  0
  4 10  2  0  0  0  0
  5  6  1  0  0  0  0
  5  8  1  0  0  0  0
  5  9  1  0  0  0  0
  6  7  1  0  0  0  0
  7 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0001469

> <DATABASE_NAME>
NP-MRD

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

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

> <INCHI_KEY>
AQYCMVICBNBXNA-UHFFFAOYSA-N

> <FORMULA>
C6H10O4

> <MOLECULAR_WEIGHT>
146.1412

> <EXACT_MASS>
146.057908808

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.956525275740471

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-methylpentanedioic acid

> <ALOGPS_LOGP>
0.33

> <JCHEM_LOGP>
0.5890719759999997

> <ALOGPS_LOGS>
-0.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.676174036855366

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.8942615644961274

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
32.7125

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.06e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
α-methylglutaric acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0001469 (2-Methylglutaric acid)

HMDB0000422
     RDKit          3D
2-Methylglutaric acid
 20 19  0  0  0  0  0  0  0  0999 V2000
   -1.2582   -1.4926   -0.6851 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1097   -0.2330    0.0961 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1451    0.5332   -0.2306 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3773   -0.2946    0.0522 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5884    0.4956   -0.2825 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4746    1.6732   -0.7291 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8675    0.0081   -0.1309 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2783    0.6224   -0.0998 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2057    0.2250   -0.8500 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4505    1.8662    0.4891 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5733   -2.2751   -0.3041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1433   -1.2959   -1.7693 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3232   -1.8369   -0.5611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0575   -0.4779    1.1952 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1617    1.4189    0.4449 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1706    0.8615   -1.2727 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2933   -1.2211   -0.5450 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3896   -0.5453    1.1197 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1145   -0.7656    0.4711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1826    2.7338    0.0269 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  1  0
  5  6  2  0
  5  7  1  0
  2  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
  4 17  1  0
  4 18  1  0
  7 19  1  0
 10 20  1  0
M  END
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PDB for NP0001469 (2-Methylglutaric acid)

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  O   UNK     0      20.522 -17.659   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      19.188 -15.349   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      12.519 -17.659   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      13.853 -15.349   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      17.854 -17.659   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      16.521 -16.889   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      15.187 -17.659   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      17.854 -19.199   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      19.188 -16.889   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      13.853 -16.889   0.000  0.00  0.00           C+0
CONECT    1    9                                                            
CONECT    2    9                                                            
CONECT    3   10                                                            
CONECT    4   10                                                            
CONECT    5    6    8    9                                                  
CONECT    6    5    7                                                       
CONECT    7    6   10                                                       
CONECT    8    5                                                            
CONECT    9    1    2    5                                                  
CONECT   10    3    4    7                                                  
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for NP0001469 (2-Methylglutaric acid)

COMPND    HMDB0000422
HETATM    1  C1  UNL     1      -1.258  -1.493  -0.685  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.110  -0.233   0.096  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.145   0.533  -0.231  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.377  -0.295   0.052  1.00  0.00           C  
HETATM    5  C5  UNL     1       2.588   0.496  -0.282  1.00  0.00           C  
HETATM    6  O1  UNL     1       2.475   1.673  -0.729  1.00  0.00           O  
HETATM    7  O2  UNL     1       3.867   0.008  -0.131  1.00  0.00           O  
HETATM    8  C6  UNL     1      -2.278   0.622  -0.100  1.00  0.00           C  
HETATM    9  O3  UNL     1      -3.206   0.225  -0.850  1.00  0.00           O  
HETATM   10  O4  UNL     1      -2.451   1.866   0.489  1.00  0.00           O  
HETATM   11  H1  UNL     1      -0.573  -2.275  -0.304  1.00  0.00           H  
HETATM   12  H2  UNL     1      -1.143  -1.296  -1.769  1.00  0.00           H  
HETATM   13  H3  UNL     1      -2.323  -1.837  -0.561  1.00  0.00           H  
HETATM   14  H4  UNL     1      -1.057  -0.478   1.195  1.00  0.00           H  
HETATM   15  H5  UNL     1       0.162   1.419   0.445  1.00  0.00           H  
HETATM   16  H6  UNL     1       0.171   0.862  -1.273  1.00  0.00           H  
HETATM   17  H7  UNL     1       1.293  -1.221  -0.545  1.00  0.00           H  
HETATM   18  H8  UNL     1       1.390  -0.545   1.120  1.00  0.00           H  
HETATM   19  H9  UNL     1       4.115  -0.766   0.471  1.00  0.00           H  
HETATM   20  H10 UNL     1      -2.183   2.734   0.027  1.00  0.00           H  
CONECT    1    2   11   12   13
CONECT    2    3    8   14
CONECT    3    4   15   16
CONECT    4    5   17   18
CONECT    5    6    6    7
CONECT    7   19
CONECT    8    9    9   10
CONECT   10   20
END
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SMILES for NP0001469 (2-Methylglutaric acid)

CC(CCC(O)=O)C(O)=O
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INCHI for NP0001469 (2-Methylglutaric acid)

InChI=1S/C6H10O4/c1-4(6(9)10)2-3-5(7)8/h4H,2-3H2,1H3,(H,7,8)(H,9,10)
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View in JSmolView NMR Assignments
Synonyms
ValueSource
alpha-Methylglutaric acidChEBI
a-MethylglutarateGenerator
a-Methylglutaric acidGenerator
alpha-MethylglutarateGenerator
Α-methylglutarateGenerator
Α-methylglutaric acidGenerator
2-MethylglutarateGenerator
(+-)-2-Methylglutaric acidHMDB
2-MethylpentanedioateHMDB
2-Methylpentanedioic acidHMDB
2-Methyleneglutaric acidHMDB
2-MethyleneglutarateHMDB
alpha-Methylene glutarateHMDB
alpha-Methylene glutarate, ion(2-)HMDB
2-Methylene glutarateHMDB
2-Methyl-glutarateHMDB
(2)-MethylglutarateGenerator
Chemical FormulaC6H10O4
Average Mass146.1412 Da
Monoisotopic Mass146.05791 Da
IUPAC Name2-methylpentanedioic acid
Traditional Nameα-methylglutaric acid
CAS Registry Number617-62-9
SMILES
CC(CCC(O)=O)C(O)=O
InChI Identifier
InChI=1S/C6H10O4/c1-4(6(9)10)2-3-5(7)8/h4H,2-3H2,1H3,(H,7,8)(H,9,10)
InChI KeyAQYCMVICBNBXNA-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, simulated)Ahselim2022-01-10View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Species Where Detected
Species NameSourceReference
Homo sapiens (Urine)KNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as methyl-branched fatty acids. These are fatty acids with an acyl chain that has a methyl branch. Usually, they are saturated and contain only one or more methyl group. However, branches other than methyl may be present.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentMethyl-branched fatty acids
Alternative Parents
Substituents
  • Methyl-branched fatty acid
  • Dicarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility908 mg/mLNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility40.6 g/LALOGPS
logP0.33ALOGPS
logP0.59ChemAxon
logS-0.56ALOGPS
pKa (Strongest Acidic)3.89ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity32.71 m³·mol⁻¹ChemAxon
Polarizability13.96 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000422
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022036
KNApSAcK IDC00052128
Chemspider ID11549
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5411
PubChem Compound12046
PDB IDNot Available
ChEBI ID68567
Good Scents IDNot Available
References
General References
  1. McKenna EJ, Kallio RE: Microbial metabolism of the isoprenoid alkane pristane. Proc Natl Acad Sci U S A. 1971 Jul;68(7):1552-4. doi: 10.1073/pnas.68.7.1552. [PubMed:4327007 ]
  2. Le TN, Mikolasch A, Awe S, Sheikhany H, Klenk HP, Schauer F: Oxidation of aliphatic, branched chain, and aromatic hydrocarbons by Nocardia cyriacigeorgica isolated from oil-polluted sand samples collected in the Saudi Arabian Desert. J Basic Microbiol. 2010 Jun;50(3):241-53. doi: 10.1002/jobm.200900358. [PubMed:20143352 ]