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Showing NP-Card for Methylglutaric acid (NP0000036)

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Record Information
Version1.0
Created at2005-11-16 15:48:42 UTC
Updated at2020-11-24 22:12:19 UTC
NP-MRD IDNP0000036
Secondary Accession NumbersNone
Natural Product Identification
Common NameMethylglutaric 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000036 (Methylglutaric acid)


  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 NP0000036 (Methylglutaric acid)

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
Download

3D SDF for NP0000036 (Methylglutaric acid)


  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>
NP0000036

> <DATABASE_NAME>
NP-MRD

> <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

$$$$
Download

3D-SDF for NP0000036 (Methylglutaric acid)

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 NP0000036 (Methylglutaric acid)

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 NP0000036 (Methylglutaric acid)

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 NP0000036 (Methylglutaric acid)

CC(CC(O)=O)CC(O)=O
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INCHI for NP0000036 (Methylglutaric acid)

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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View in JSmol
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
Chemical FormulaC6H10O4
Average Mass146.1412 Da
Monoisotopic Mass146.05791 Da
IUPAC Name3-methylpentanedioic acid
Traditional Namemethylglutaric acid
CAS Registry Number626-51-7
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
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
Crotalaria duraKNApSAcK Database
Crotalaria globiferaKNApSAcK Database
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Salmonella entericaLOTUS Database
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Triticum aestivumKNApSAcK 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 Point80 - 82 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility36.9 g/LALOGPS
logP0.33ALOGPS
logP0.33ChemAxon
logS-0.6ALOGPS
pKa (Strongest Acidic)3.91ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity32.69 m³·mol⁻¹ChemAxon
Polarizability13.88 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000752
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022224
KNApSAcK IDC00001187
Chemspider ID11781
KEGG Compound IDNot Available
BioCyc IDCPD-516
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5720
PubChem Compound12284
PDB IDNot Available
ChEBI ID68566
Good Scents IDNot Available
References
General References
  1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
  2. Guneral F, Bachmann C: Age-related reference values for urinary organic acids in a healthy Turkish pediatric population. Clin Chem. 1994 Jun;40(6):862-6. [PubMed:8087979 ]
  3. Truscott RJ, Halpern B, Wysocki SJ, Hahnel R, Wilcken B: Studies on a child suspected of having a dficiency in 3-hydroxy-3-methylglutaryl-Co A lyase. Clin Chim Acta. 1979 Jul 2;95(1):11-16. [PubMed:509721 ]
  4. Sheffer RN, Zlotogora J, Elpeleg ON, Raz J, Ben-Ezra D: Behr's syndrome and 3-methylglutaconic aciduria. Am J Ophthalmol. 1992 Oct 15;114(4):494-7. [PubMed:1384336 ]
  5. Duran M, Beemer FA, Tibosch AS, Bruinvis L, Ketting D, Wadman SK: Inherited 3-methylglutaconic aciduria in two brothers--another defect of leucine metabolism. J Pediatr. 1982 Oct;101(4):551-4. [PubMed:6181239 ]