Showing NP-Card for Mesaconic acid (NP0000567)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2025-02-11 15:41:39 UTC
NP-MRD IDNP0000567
Secondary Accession NumbersNone
Natural Product Identification
Common NameMesaconic acid
DescriptionMesaconic acid, also known as 2-methylfumarate or citronic acid, 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. Mesaconic acid is a dicarboxylic butenoic acid, with a methyl group in position 2 and the double bound between carbons 2 and 3. Mesaconic acid was first studied for its physical properties in 1874 by Jacobus van ‘t Hoff (https://Web.Archive.Org/web/20051117102410/http://Dbhs.Wvusd.K12.Ca.Us/webdocs/Chem-History/Van%27t-Hoff-1874.Html). It is now known to be involved in the biosynthesis of vitamin B12 and it is also a competitor inhibitor of the reduction of fumarate.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000567 (Mesaconic acid)

  Mrv1652305271900202D          

  9  8  0  0  0  0            999 V2000
   -2.0087    0.2785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7232   -0.1339    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0087    1.1035    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2942   -0.1339    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2942   -0.9589    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5798    0.2785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1346   -0.1339    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1346   -0.9589    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8491    0.2785    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  6  7  1  0  0  0  0
  1  3  2  0  0  0  0
  2  1  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
M  END
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3D MOL for NP0000567 (Mesaconic acid)

HMDB0000749
     RDKit          3D
Mesaconic acid
 15 14  0  0  0  0  0  0  0  0999 V2000
   -0.0546    1.1373    0.8746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5199    0.0960   -0.0503 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3792   -0.6398   -0.6986 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7898   -0.4114   -0.4903 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6457   -1.1216   -1.1160 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3062    0.5342    0.3501 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9363   -0.1657   -0.2883 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7659    0.5381    0.3320 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4157   -1.1344   -1.1488 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4834    1.9793    0.3680 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9778    1.6453    1.2893 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4733    0.7713    1.7621 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0616   -1.4257   -1.3965 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8003    0.3349    1.2221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2692   -2.1377   -1.0094 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  2  0
  4  6  1  0
  2  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  3 13  1  0
  6 14  1  0
  9 15  1  0
M  END
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3D SDF for NP0000567 (Mesaconic acid)

  Mrv1652305271900202D          

  9  8  0  0  0  0            999 V2000
   -2.0087    0.2785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7232   -0.1339    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0087    1.1035    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2942   -0.1339    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2942   -0.9589    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5798    0.2785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1346   -0.1339    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1346   -0.9589    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8491    0.2785    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  6  7  1  0  0  0  0
  1  3  2  0  0  0  0
  2  1  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000567

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H6O4/c1-3(5(8)9)2-4(6)7/h2H,1H3,(H,6,7)(H,8,9)/b3-2+

> <INCHI_KEY>
HNEGQIOMVPPMNR-NSCUHMNNSA-N

> <FORMULA>
C5H6O4

> <MOLECULAR_WEIGHT>
130.0987

> <EXACT_MASS>
130.02660868

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
11.241128315164042

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
0.21

> <JCHEM_LOGP>
0.35463615800000003

> <ALOGPS_LOGS>
-0.91

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.568292663140774

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.722300394674801

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
28.964100000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.59e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
mesaconic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0000567 (Mesaconic acid)

HMDB0000749
     RDKit          3D
Mesaconic acid
 15 14  0  0  0  0  0  0  0  0999 V2000
   -0.0546    1.1373    0.8746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5199    0.0960   -0.0503 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3792   -0.6398   -0.6986 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7898   -0.4114   -0.4903 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6457   -1.1216   -1.1160 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3062    0.5342    0.3501 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9363   -0.1657   -0.2883 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7659    0.5381    0.3320 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4157   -1.1344   -1.1488 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4834    1.9793    0.3680 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9778    1.6453    1.2893 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4733    0.7713    1.7621 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0616   -1.4257   -1.3965 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8003    0.3349    1.2221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2692   -2.1377   -1.0094 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  2  0
  4  6  1  0
  2  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  3 13  1  0
  6 14  1  0
  9 15  1  0
M  END
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PDB for NP0000567 (Mesaconic 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  C   UNK     0      -3.750   0.520   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -5.083  -0.250   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      -3.750   2.060   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -2.416  -0.250   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.416  -1.790   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.082   0.520   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.251  -0.250   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       0.251  -1.790   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       1.585   0.520   0.000  0.00  0.00           O+0
CONECT    1    4    3    2                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for NP0000567 (Mesaconic acid)

COMPND    HMDB0000749
HETATM    1  C1  UNL     1      -0.055   1.137   0.875  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.520   0.096  -0.050  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.379  -0.640  -0.699  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.790  -0.411  -0.490  1.00  0.00           C  
HETATM    5  O1  UNL     1       2.646  -1.122  -1.116  1.00  0.00           O  
HETATM    6  O2  UNL     1       2.306   0.534   0.350  1.00  0.00           O  
HETATM    7  C5  UNL     1      -1.936  -0.166  -0.288  1.00  0.00           C  
HETATM    8  O3  UNL     1      -2.766   0.538   0.332  1.00  0.00           O  
HETATM    9  O4  UNL     1      -2.416  -1.134  -1.149  1.00  0.00           O  
HETATM   10  H1  UNL     1       0.483   1.979   0.368  1.00  0.00           H  
HETATM   11  H2  UNL     1      -0.978   1.645   1.289  1.00  0.00           H  
HETATM   12  H3  UNL     1       0.473   0.771   1.762  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.062  -1.426  -1.397  1.00  0.00           H  
HETATM   14  H5  UNL     1       2.800   0.335   1.222  1.00  0.00           H  
HETATM   15  H6  UNL     1      -2.269  -2.138  -1.009  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3    3    7
CONECT    3    4   13
CONECT    4    5    5    6
CONECT    6   14
CONECT    7    8    8    9
CONECT    9   15
END
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SMILES for NP0000567 (Mesaconic acid)

C\C(=C/C(O)=O)C(O)=O
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INCHI for NP0000567 (Mesaconic acid)

InChI=1S/C5H6O4/c1-3(5(8)9)2-4(6)7/h2H,1H3,(H,6,7)(H,8,9)/b3-2+
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Synonyms
Chemical FormulaC5H6O4
Average Mass130.0987 Da
Monoisotopic Mass130.02661 Da
IUPAC Name(2E)-2-methylbut-2-enedioic acid
Traditional Namemesaconic acid
CAS Registry Number498-24-8
SMILES
C\C(=C/C(O)=O)C(O)=O
InChI Identifier
InChI=1S/C5H6O4/c1-3(5(8)9)2-4(6)7/h2H,1H3,(H,6,7)(H,8,9)/b3-2+
InChI KeyHNEGQIOMVPPMNR-NSCUHMNNSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
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
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, simulated)varshavi.d26@gmail.comNot AvailableNot Available2021-08-08View Spectrum
Species
Species of Origin
Species NameSourceReference
Homo sapiens (Serum)Animalia
Homo sapiens (Urine)Animalia
Saccharum sinensisKNApSAcK Database
Saxifraga stoloniferaLOTUS Database
Solanum tuberosumKNApSAcK Database
Trypanosoma bruceiLOTUS 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
  • 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
StateSolid
Experimental Properties
PropertyValueReference
Melting Point200 - 202 °CNot Available
Boiling Point336.60 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility26.3 mg/mL at 18 °CNot Available
LogP0.540 (est)The Good Scents Company Information System
Predicted Properties
PropertyValueSource
Water Solubility15.9 g/LALOGPS
logP0.21ALOGPS
logP0.35ChemAxon
logS-0.91ALOGPS
pKa (Strongest Acidic)3.72ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity28.96 m³·mol⁻¹ChemAxon
Polarizability11.24 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000749
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022221
KNApSAcK IDC00051539
Chemspider ID10289044
KEGG Compound IDC01732
BioCyc IDNot Available
BiGG ID38272
Wikipedia LinkMesaconic_acid
METLIN ID4130
PubChem Compound638129
PDB IDMEZ
ChEBI ID16600
Good Scents IDrw1257141
References
General References