Showing NP-Card for (E)-2-Methylglutaconic acid (NP0086927)

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Record Information
Version2.0
Created at2022-05-11 16:34:53 UTC
Updated at2022-05-11 16:34:53 UTC
NP-MRD IDNP0086927
Secondary Accession NumbersNone
Natural Product Identification
Common Name(E)-2-Methylglutaconic acid
Description(E)-2-Methylglutaconic acid, also known as (e)-2-methyl-2-pentenedioate or trans-2-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. (E)-2-Methylglutaconic acid was first documented in 1982 (PMID: 7059658). However, branches other than methyl may be present (E)-2-Methylglutaconic acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0086927 ((E)-2-Methylglutaconic acid)

  Mrv0541 02231219272D          

 10  9  0  0  0  0            999 V2000
   24.9818  -13.2676    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.6953  -13.2676    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   24.2675  -12.0301    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.4097  -12.0301    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.5530  -13.2676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.1242  -14.0925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.2675  -12.8550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.4097  -12.8550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.1242  -13.2676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.8386  -12.8550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  2  8  1  0  0  0  0
  3  7  2  0  0  0  0
  4  8  2  0  0  0  0
  5  7  1  0  0  0  0
  5 10  1  0  0  0  0
  6  9  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
M  END
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3D MOL for NP0086927 ((E)-2-Methylglutaconic acid)

     RDKit          3D

 18 17  0  0  0  0  0  0  0  0999 V2000
    1.0424   -1.4715   -0.3081 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9141   -0.0752    0.1230 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2831    0.4025    0.3986 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5418   -0.3767    0.3048 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4072    0.3299   -0.6710 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1683    0.2556   -1.8931 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4938    1.0851   -0.2543 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0885    0.7789    0.2480 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0241    1.9771    0.6136 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3294    0.2456   -0.0493 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7655   -1.5984   -1.3919 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5021   -2.1923    0.3327 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1254   -1.7956   -0.2274 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3257    1.4448    0.7149 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0629   -0.3535    1.2892 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3442   -1.4269   -0.0204 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3551    1.9976    0.2050 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1908    0.7731    0.1076 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  7  1  0
  5  6  2  0
  2  8  1  0
  8 10  1  0
  8  9  2  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  7 17  1  0
 10 18  1  0
M  END
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3D SDF for NP0086927 ((E)-2-Methylglutaconic acid)

  Mrv0541 02231219272D          

 10  9  0  0  0  0            999 V2000
   24.9818  -13.2676    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.6953  -13.2676    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   24.2675  -12.0301    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.4097  -12.0301    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.5530  -13.2676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.1242  -14.0925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.2675  -12.8550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.4097  -12.8550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.1242  -13.2676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.8386  -12.8550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  2  8  1  0  0  0  0
  3  7  2  0  0  0  0
  4  8  2  0  0  0  0
  5  7  1  0  0  0  0
  5 10  1  0  0  0  0
  6  9  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0086927

> <DATABASE_NAME>
NP-MRD

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

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

> <INCHI_KEY>
JKGHDBJDBRBRNA-DUXPYHPUSA-N

> <FORMULA>
C6H8O4

> <MOLECULAR_WEIGHT>
144.1253

> <EXACT_MASS>
144.042258744

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
13.133648001496638

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
0.30

> <JCHEM_LOGP>
0.43945967666666647

> <ALOGPS_LOGS>
-1.22

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.63141875737817

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.83570068851202

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
33.5884

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.75e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2E-methyl-glutaconic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0086927 ((E)-2-Methylglutaconic acid)

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PDB for NP0086927 ((E)-2-Methylglutaconic acid)
HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      46.633 -24.766   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      38.631 -24.766   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      45.299 -22.456   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      39.965 -22.456   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      43.966 -24.766   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      41.299 -26.306   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      45.299 -23.996   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      39.965 -23.996   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      41.299 -24.766   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      42.632 -23.996   0.000  0.00  0.00           C+0
CONECT    1    7                                                            
CONECT    2    8                                                            
CONECT    3    7                                                            
CONECT    4    8                                                            
CONECT    5    7   10                                                       
CONECT    6    9                                                            
CONECT    7    1    3    5                                                  
CONECT    8    2    4    9                                                  
CONECT    9    6    8   10                                                  
CONECT   10    5    9                                                       
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END

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3D PDB for NP0086927 ((E)-2-Methylglutaconic acid)
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SMILES for NP0086927 ((E)-2-Methylglutaconic acid)
C\C(=C/CC(O)=O)C(O)=O
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INCHI for NP0086927 ((E)-2-Methylglutaconic acid)
InChI=1S/C6H8O4/c1-4(6(9)10)2-3-5(7)8/h2H,3H2,1H3,(H,7,8)(H,9,10)/b4-2+
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View in JSmol
Synonyms
ValueSource
(e)-2-MethylglutaconateGenerator
(e)-2-Methyl-2-pentenedioateHMDB
(e)-2-Methyl-2-pentenedioic acidHMDB
trans-2-MethylglutaconateHMDB
trans-2-Methylglutaconic acidHMDB
1-Methyl-1-propene-1,3-dicarboxylic acidHMDB
2-Methylglutaconic acidHMDB
2E-Methyl-glutaconateHMDB
(e)-2-Methylglutaconic acidMeSH
Chemical FormulaC6H8O4
Average Mass144.1253 Da
Monoisotopic Mass144.04226 Da
IUPAC Name(2E)-2-methylpent-2-enedioic acid
Traditional Name2E-methyl-glutaconic acid
CAS Registry NumberNot Available
SMILES
C\C(=C/CC(O)=O)C(O)=O
InChI Identifier
InChI=1S/C6H8O4/c1-4(6(9)10)2-3-5(7)8/h2H,3H2,1H3,(H,7,8)(H,9,10)/b4-2+
InChI KeyJKGHDBJDBRBRNA-DUXPYHPUSA-N
Experimental Spectra
Not Available
Predicted Spectra
Chemical Shift Submissions
Not Available
Species
Species of Origin
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
logP0.3ALOGPS
logP0.44ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)3.84ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity33.59 m³·mol⁻¹ChemAxon
Polarizability13.13 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0002266  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022936  
KNApSAcK IDNot Available
Chemspider ID4897953  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID6584  
PubChem Compound6368126  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Duran M, Bruinvis L, Ketting D, Kamerling JP, Wadman SK, Schutgens RB: The identification of (E)-2-methylglutaconic acid, a new isoleucine metabolite, in the urine of patients with beta-ketothiolase deficiency, propionic acidaemia and methylmalonic acidaemia. Biomed Mass Spectrom. 1982 Jan;9(1):1-5. doi: 10.1002/bms.1200090102. [PubMed:7059658  ]