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Showing NP-Card for Methylsuccinic acid (NP0000069)

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Record Information
Version1.0
Created at2006-02-02 11:25:17 UTC
Updated at2021-10-07 20:41:28 UTC
NP-MRD IDNP0000069
Secondary Accession NumbersNone
Natural Product Identification
Common NameMethylsuccinic acid
DescriptionMethylsuccinic acid (CAS: 498-21-5) Is a normal metabolite found in human fluids. Increased urinary levels of methylsuccinic acid (together with ethylmalonic acid) are the main biochemical measurable features in ethylmalonic encephalopathy (OMIM: 602473 ), A rare metabolic disorder with an autosomal recessive mode of inheritance that is clinically characterized by neuromotor delay, hyperlactic acidemia, recurrent petechiae, orthostatic acrocyanosis, and chronic diarrhea (PMID: 12382164 ). The underlying biochemical defect involves isoleucine catabolism (PMID: 9667231 ). Methylsuccinic acid levels were found to have decreased in the urine of animals under D-serine-induced nephrotoxicity (D-serine causes selective necrosis of the proximal straight tubules in the rat kidney) (PMID: 15596249 ). Moreover, methylsuccinic acid is found to be associated with ethylmalonic encephalopathy, isovaleric acidemia, and medium-chain acyl-CoA dehydrogenase deficiency, which are also inborn errors of metabolism.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000069 (Methylsuccinic acid)


  Mrv1652303172016322D          

  9  8  0  0  1  0            999 V2000
    1.7069   -0.0228    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8656   -0.4353    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9924   -1.2604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1511    0.8022    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2778   -0.0228    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4366   -0.4353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2778    0.8022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9924   -0.4353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1511   -0.0228    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  1  0  0  0  0
  2  9  1  0  0  0  0
  3  8  2  0  0  0  0
  4  9  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  6  0  0  0
  5  8  1  0  0  0  0
  6  9  1  0  0  0  0
M  END
Download

3D MOL for NP0000069 (Methylsuccinic acid)

HMDB0001844
     RDKit          3D
Methylsuccinic acid
 17 16  0  0  0  0  0  0  0  0999 V2000
    0.9049   -0.8327   -0.6174 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4240    0.4564    0.0334 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9668    0.2498    0.6040 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9147   -0.1302   -0.4693 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3657    0.7916   -1.2296 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3229   -1.4387   -0.6728 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3818    0.7655    1.1286 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9654    0.8438    2.2975 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7169    0.9564    0.7999 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4727   -1.7283   -0.1110 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0112   -0.9222   -0.5420 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6606   -0.8798   -1.6997 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4274    1.2222   -0.7638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3145    1.2152    1.0069 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9665   -0.5182    1.3983 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1390   -1.6380   -1.2289 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0253    1.5873    0.0660 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  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  6
  3 14  1  0
  3 15  1  0
  6 16  1  0
  9 17  1  0
M  END
Download

3D SDF for NP0000069 (Methylsuccinic acid)


  Mrv1652303172016322D          

  9  8  0  0  1  0            999 V2000
    1.7069   -0.0228    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8656   -0.4353    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9924   -1.2604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1511    0.8022    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2778   -0.0228    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4366   -0.4353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2778    0.8022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9924   -0.4353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1511   -0.0228    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  1  0  0  0  0
  2  9  1  0  0  0  0
  3  8  2  0  0  0  0
  4  9  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  6  0  0  0
  5  8  1  0  0  0  0
  6  9  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000069

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H](CC(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O4/c1-3(5(8)9)2-4(6)7/h3H,2H2,1H3,(H,6,7)(H,8,9)/t3-/m0/s1

> <INCHI_KEY>
WXUAQHNMJWJLTG-VKHMYHEASA-N

> <FORMULA>
C5H8O4

> <MOLECULAR_WEIGHT>
132.115

> <EXACT_MASS>
132.042258738

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
11.866190114358801

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-methylbutanedioic acid

> <ALOGPS_LOGP>
0.13

> <JCHEM_LOGP>
0.14450331100000002

> <ALOGPS_LOGS>
-0.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.578119667709393

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.9897992068502925

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
28.1115

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.03e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-methylbutanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000069 (Methylsuccinic acid)

HMDB0001844
     RDKit          3D
Methylsuccinic acid
 17 16  0  0  0  0  0  0  0  0999 V2000
    0.9049   -0.8327   -0.6174 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4240    0.4564    0.0334 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9668    0.2498    0.6040 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9147   -0.1302   -0.4693 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3657    0.7916   -1.2296 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3229   -1.4387   -0.6728 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3818    0.7655    1.1286 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9654    0.8438    2.2975 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7169    0.9564    0.7999 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4727   -1.7283   -0.1110 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0112   -0.9222   -0.5420 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6606   -0.8798   -1.6997 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4274    1.2222   -0.7638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3145    1.2152    1.0069 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9665   -0.5182    1.3983 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1390   -1.6380   -1.2289 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0253    1.5873    0.0660 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  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  6
  3 14  1  0
  3 15  1  0
  6 16  1  0
  9 17  1  0
M  END
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PDB for NP0000069 (Methylsuccinic acid)

HEADER    PROTEIN                                 17-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-MAR-20         0                                  
HETATM    1  O   UNK     0       3.186  -0.043   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      -3.483  -0.813   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       1.852  -2.353   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      -2.149   1.497   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.519  -0.043   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.815  -0.813   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.519   1.497   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.852  -0.813   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.149  -0.043   0.000  0.00  0.00           C+0
CONECT    1    8                                                            
CONECT    2    9                                                            
CONECT    3    8                                                            
CONECT    4    9                                                            
CONECT    5    6    7    8                                                  
CONECT    6    5    9                                                       
CONECT    7    5                                                            
CONECT    8    1    3    5                                                  
CONECT    9    2    4    6                                                  
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for NP0000069 (Methylsuccinic acid)

COMPND    HMDB0001844
HETATM    1  C1  UNL     1       0.905  -0.833  -0.617  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.424   0.456   0.033  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.967   0.250   0.604  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.915  -0.130  -0.469  1.00  0.00           C  
HETATM    5  O1  UNL     1      -2.366   0.792  -1.230  1.00  0.00           O  
HETATM    6  O2  UNL     1      -2.323  -1.439  -0.673  1.00  0.00           O  
HETATM    7  C5  UNL     1       1.382   0.765   1.129  1.00  0.00           C  
HETATM    8  O3  UNL     1       0.965   0.844   2.297  1.00  0.00           O  
HETATM    9  O4  UNL     1       2.717   0.956   0.800  1.00  0.00           O  
HETATM   10  H1  UNL     1       0.473  -1.728  -0.111  1.00  0.00           H  
HETATM   11  H2  UNL     1       2.011  -0.922  -0.542  1.00  0.00           H  
HETATM   12  H3  UNL     1       0.661  -0.880  -1.700  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.427   1.222  -0.764  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.314   1.215   1.007  1.00  0.00           H  
HETATM   15  H6  UNL     1      -0.967  -0.518   1.398  1.00  0.00           H  
HETATM   16  H7  UNL     1      -3.139  -1.638  -1.229  1.00  0.00           H  
HETATM   17  H8  UNL     1       3.025   1.587   0.066  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3    7   13
CONECT    3    4   14   15
CONECT    4    5    5    6
CONECT    6   16
CONECT    7    8    8    9
CONECT    9   17
END
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SMILES for NP0000069 (Methylsuccinic acid)

C[C@@H](CC(O)=O)C(O)=O
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INCHI for NP0000069 (Methylsuccinic acid)

InChI=1S/C5H8O4/c1-3(5(8)9)2-4(6)7/h3H,2H2,1H3,(H,6,7)(H,8,9)/t3-/m0/s1
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View in JSmol
Synonyms
ValueSource
(S)-2-Methylbutanedioic acidChEBI
(S)-2-MethylbutanedioateGenerator
MethylsuccinateGenerator
(S)-MethylsuccinateHMDB
(-)-(2S)-Methylbutanedioic acidHMDB
(-)-(S)-alpha-Methylsuccinic acidHMDB
(-)-(S)-Α-methylsuccinic acidHMDB
(-)-2-Methylsuccinic acidHMDB
(-)-Methylsuccinic acidHMDB
(-)-alpha-Methylsuccinic acidHMDB
(-)-Α-methylsuccinic acidHMDB
(2S)-2-Methylbutanedioic acidHMDB
(2S)-Methylbutanedioic acidHMDB
(S)-(-)-2-Methylsuccinic acidHMDB
(S)-(-)-Methylsuccinic acidHMDB
(S)-2-Methylsuccinic acidHMDB
(S)-Methylsuccinic acidHMDB
(S)-alpha-Methylsuccinic acidHMDB
(S)-Α-methylsuccinic acidHMDB
1,2-Propanedicarboxylic acidHMDB
2-Methylbutane-1,4-dioic acidHMDB
2-Methylbutanedioic acidHMDB
2-Methylsuccinic acidHMDB
Methylbutanedioic acidHMDB
Pyrotartaric acidHMDB
alpha-Methylsuccinic acidHMDB
Α-methylsuccinic acidHMDB
Methylsuccinic acidHMDB
Chemical FormulaC5H8O4
Average Mass132.1146 Da
Monoisotopic Mass132.04226 Da
IUPAC Name(2S)-2-methylbutanedioic acid
Traditional Name(2S)-2-methylbutanedioic acid
CAS Registry Number498-21-5
SMILES
CC(CC(O)=O)C(O)=O
InChI Identifier
InChI=1S/C5H8O4/c1-3(5(8)9)2-4(6)7/h3H,2H2,1H3,(H,6,7)(H,8,9)
InChI KeyWXUAQHNMJWJLTG-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
Aloe africanaLOTUS Database
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 DescriptorsNot Available
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point117.5 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility516.5 mg/mLWishart, D. S., Tzur, D., Knox, C., Eisner, R., Guo, A. C., Young, N., ... & Querengesser, L. (2007). HMDB: the human metabolome database. Nucleic acids research, 35(suppl_1), D521-D526.
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility103 g/LALOGPS
logP0.13ALOGPS
logP0.14ChemAxon
logS-0.11ALOGPS
pKa (Strongest Acidic)3.99ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity28.11 m³·mol⁻¹ChemAxon
Polarizability11.87 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0001844
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022704
KNApSAcK IDC00052350
Chemspider ID5323413
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link2-Methylsuccinic acid
METLIN IDNot Available
PubChem Compound6950476
PDB IDNot Available
ChEBI ID91316
Good Scents IDNot Available
References
General References
  1. 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 ]
  2. Bhala A, Willi SM, Rinaldo P, Bennett MJ, Schmidt-Sommerfeld E, Hale DE: Clinical and biochemical characterization of short-chain acyl-coenzyme A dehydrogenase deficiency. J Pediatr. 1995 Jun;126(6):910-5. [PubMed:7776094 ]
  3. Grosso S, Mostardini R, Farnetani MA, Molinelli M, Berardi R, Dionisi-Vici C, Rizzo C, Morgese G, Balestri P: Ethylmalonic encephalopathy: further clinical and neuroradiological characterization. J Neurol. 2002 Oct;249(10):1446-50. [PubMed:12382164 ]
  4. Nowaczyk MJ, Lehotay DC, Platt BA, Fisher L, Tan R, Phillips H, Clarke JT: Ethylmalonic and methylsuccinic aciduria in ethylmalonic encephalopathy arise from abnormal isoleucine metabolism. Metabolism. 1998 Jul;47(7):836-9. [PubMed:9667231 ]
  5. Williams RE, Major H, Lock EA, Lenz EM, Wilson ID: D-Serine-induced nephrotoxicity: a HPLC-TOF/MS-based metabonomics approach. Toxicology. 2005 Feb 14;207(2):179-90. [PubMed:15596249 ]