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Showing NP-Card for 3-Methylglutaconic acid (NP0083444)

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Record Information
Version2.0
Created at2022-04-29 04:29:19 UTC
Updated at2023-04-27 20:30:47 UTC
NP-MRD IDNP0083444
Secondary Accession NumbersNone
Natural Product Identification
Common Name3-Methylglutaconic acid
Description3-Methylglutaconic acid, also known as b-methylglutaconate, 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. These are also the characteristic symptoms of the untreated IEMs mentioned above. 3-Methylglutaconic acid is an intermediate (as the CoA thioester) in the leucine degradative pathway as well as the mevalonate shunt, a pathway that links isoprenoid metabolism with mitochondrial acetyl-CoA metabolism (PMID: 7603789 ). 3-Methylglutaconic acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. 3-Methylglutaconyl-CoA hydratase is involved in the metabolism process of 3-methylglutaconic acid. 3-Methylglutaconic acid is a potentially toxic compound. 3-Methylglutaconic acid, with regard to humans, has been found to be associated with several diseases such as sengers syndrome, 3-methylglutaconic aciduria type VI, 3-methylglutaconic aciduria type V, and 3-methylglutaconic aciduria type IV; 3-methylglutaconic acid has also been linked to the inborn metabolic disorder 3-hydroxy-3-methylglutaryl-coa lyase deficiency. 3-Methylglutaconic acid is found in Homo sapiens (Urine). 3-Methylglutaconic acid was first documented in 1992 (PMID: 1384336). Acidosis typically occurs when arterial pH falls below 7.35 (PMID: 7479590) (PMID: 1287564) (PMID: 8494328) (PMID: 8111960) (PMID: 24407466).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0083444 (3-Methylglutaconic acid)

3-Methylglutaconic acid.mol
  Mrv1652302121822452D          

 10  9  0  0  0  0            999 V2000
    1.4289   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.6188    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.6188    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.6188    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.6188    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.6187    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.6188    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.6187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  6  2  0  0  0  0
  1  7  1  0  0  0  0
  5  8  2  0  0  0  0
  5  9  1  0  0  0  0
  3 10  1  0  0  0  0
M  END
Download

3D MOL for NP0083444 (3-Methylglutaconic acid)

     RDKit          3D

 18 17  0  0  0  0  0  0  0  0999 V2000
   -0.0360   -1.6426    0.3972 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0518   -0.2826   -0.1672 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1695    0.3845    0.0764 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2738   -0.1605    0.8546 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3031   -1.2967    1.3758 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4328    0.6083    1.0729 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9692    0.3858   -0.9603 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2642    0.5861   -0.3355 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6190    0.2499    0.8219 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2514    1.2226   -1.0794 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0074   -1.5792    1.5023 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7534   -2.2933   -0.0280 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9907   -2.1519    0.1670 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3024    1.4117   -0.3176 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8204    1.1915    0.3432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1151   -0.2125   -1.9074 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5960    1.3656   -1.3098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2731    2.2135   -1.2439 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  7  1  0
  7  8  1  0
  8 10  1  0
  8  9  2  0
  2  3  2  0
  3  4  1  0
  4  6  1  0
  4  5  2  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  7 16  1  0
  7 17  1  0
 10 18  1  0
  3 14  1  0
  6 15  1  0
M  END
Download

3D SDF for NP0083444 (3-Methylglutaconic acid)

3-Methylglutaconic acid.mol
  Mrv1652302121822452D          

 10  9  0  0  0  0            999 V2000
    1.4289   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.6188    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.6188    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.6188    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.6188    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.6187    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.6188    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.6187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  6  2  0  0  0  0
  1  7  1  0  0  0  0
  5  8  2  0  0  0  0
  5  9  1  0  0  0  0
  3 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0083444

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C(CC(O)=O)=C/C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H8O4/c1-4(2-5(7)8)3-6(9)10/h2H,3H2,1H3,(H,7,8)(H,9,10)/b4-2+

> <INCHI_KEY>
WKRBKYFIJPGYQC-DUXPYHPUSA-N

> <FORMULA>
C6H8O4

> <MOLECULAR_WEIGHT>
144.1253

> <EXACT_MASS>
144.042258744

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
13.266891782956623

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2E)-3-methylpent-2-enedioic acid

> <ALOGPS_LOGP>
0.37

> <JCHEM_LOGP>
0.287270459

> <ALOGPS_LOGS>
-1.22

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.659788519242309

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.854151000940069

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
33.5133

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.69e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
β-methylglutaconic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0083444 (3-Methylglutaconic acid)

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PDB for NP0083444 (3-Methylglutaconic acid)
HEADER    PROTEIN                                 12-FEB-18   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 3-Methylglutaconic acid.mol                       
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-FEB-18         0                                  
HETATM    1  C   UNK     0       2.667  -0.385   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -1.155   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000  -0.385   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.334  -1.155   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.667  -0.385   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.667   1.155   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       4.001  -1.155   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -2.667   1.155   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -4.001  -1.155   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       0.000   1.155   0.000  0.00  0.00           C+0
CONECT    1    2    6    7                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4   10                                                  
CONECT    4    3    5                                                       
CONECT    5    4    8    9                                                  
CONECT    6    1                                                            
CONECT    7    1                                                            
CONECT    8    5                                                            
CONECT    9    5                                                            
CONECT   10    3                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END

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3D PDB for NP0083444 (3-Methylglutaconic acid)
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SMILES for NP0083444 (3-Methylglutaconic acid)
C\C(CC(O)=O)=C/C(O)=O
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INCHI for NP0083444 (3-Methylglutaconic acid)
InChI=1S/C6H8O4/c1-4(2-5(7)8)3-6(9)10/h2H,3H2,1H3,(H,7,8)(H,9,10)/b4-2+
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View in JSmol
Synonyms
ValueSource
3-MethylglutaconateGenerator
b-MethylglutaconateHMDB
b-Methylglutaconic acidHMDB
beta-MethylglutaconateHMDB
beta-Methylglutaconic acidHMDB
Β-methylglutaconic acidHMDB
3-Methyl-2-pentenedioic acidHMDB
3E-MethylglutaconateHMDB
3-Methylglutaconic acidHMDB, MeSH
Chemical FormulaC6H8O4
Average Mass144.1253 Da
Monoisotopic Mass144.04226 Da
IUPAC Name(2E)-3-methylpent-2-enedioic acid
Traditional Nameβ-methylglutaconic acid
CAS Registry NumberNot Available
SMILES
C\C(CC(O)=O)=C/C(O)=O
InChI Identifier
InChI=1S/C6H8O4/c1-4(2-5(7)8)3-6(9)10/h2H,3H2,1H3,(H,7,8)(H,9,10)/b4-2+
InChI KeyWKRBKYFIJPGYQC-DUXPYHPUSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, simulated)Ahselim2023-04-27View 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 NMR1H NMR Spectrum (1D, 100 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 NMR1H NMR Spectrum (1D, 1000 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 NMR1H NMR Spectrum (1D, 200 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 NMR1H NMR Spectrum (1D, 300 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 NMR1H NMR Spectrum (1D, 400 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 NMR1H NMR Spectrum (1D, 500 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 NMR1H NMR Spectrum (1D, 600 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 NMR1H NMR Spectrum (1D, 700 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 NMR1H NMR Spectrum (1D, 800 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
1D NMR1H NMR Spectrum (1D, 900 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
Homo sapiens (Urine)Animalia
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
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
    • 

  • Unsaturated 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
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP0.37ALOGPS
logP0.29ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)3.85ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity33.51 m³·mol⁻¹ChemAxon
Polarizability13.27 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000522  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022090  
KNApSAcK IDNot Available
Chemspider ID1267861  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link3-Methylglutaconic acid  
METLIN ID5507  
PubChem Compound1551553  
PDB IDNot Available
ChEBI ID37245  
Good Scents IDNot Available
References
General References
  1. Mitchell GA, Jakobs C, Gibson KM, Robert MF, Burlina A, Dionisi-Vici C, Dallaire L: Molecular prenatal diagnosis of 3-hydroxy-3-methylglutaryl CoA lyase deficiency. Prenat Diagn. 1995 Aug;15(8):725-9. [PubMed:7479590  ] 
  2. 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  ] 
  3. Holme E, Greter J, Jacobson CE, Larsson NG, Lindstedt S, Nilsson KO, Oldfors A, Tulinius M: Mitochondrial ATP-synthase deficiency in a child with 3-methylglutaconic aciduria. Pediatr Res. 1992 Dec;32(6):731-5. doi: 10.1203/00006450-199212000-00022. [PubMed:1287564  ] 
  4. Costeff H, Elpeleg O, Apter N, Divry P, Gadoth N: 3-Methylglutaconic aciduria in "optic atrophy plus". Ann Neurol. 1993 Jan;33(1):103-4. doi: 10.1002/ana.410330117. [PubMed:8494328  ] 
  5. Kelley RI: Quantification of 3-methylglutaconic acid in urine, plasma, and amniotic fluid by isotope-dilution gas chromatography/mass spectrometry. Clin Chim Acta. 1993 Nov 15;220(2):157-64. doi: 10.1016/0009-8981(93)90044-5. [PubMed:8111960  ] 
  6. Su B, Ryan RO: Metabolic biology of 3-methylglutaconic acid-uria: a new perspective. J Inherit Metab Dis. 2014 May;37(3):359-68. doi: 10.1007/s10545-013-9669-0. Epub  2014 Jan 10. [PubMed:24407466  ]