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Showing NP-Card for Ethylmalonic acid (NP0001309)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2020-11-24 22:22:25 UTC
NP-MRD IDNP0001309
Secondary Accession NumbersNone
Natural Product Identification
Common NameEthylmalonic acid
DescriptionEthylmalonic acid, also known as alpha-carboxybutyric acid or ethylmalonate, is a member of the class of compounds known as branched fatty acids. Branched fatty acids are fatty acids containing one or more branched chains. Ethylmalonic acid is soluble (in water) and a moderately acidic compound (based on its pKa). Ethylmalonic acid can be synthesized from malonic acid, and can be synthesized into (S)-ethylmalonyl-CoA and (R)-ethylmalonyl-CoA. Ethylmalonic acid can be found in blood, cerebrospinal fluid (CSF), and urine, as well as in human fibroblasts, prostate, and skeletal muscle tissues. Moreover, ethylmalonic acid is found to be associated with anorexia nervosa and malonyl-CoA decarboxylase deficiency. Ethylmalonic acid is a non-carcinogenic (not listed by IARC) potentially toxic compound. Chronically high levels of ethylmalonic acid are associated with at least two inborn errors of metabolism, including short chain acyl CoA dehydrogenase deficiency (SCAD deficiency) and ethylmalonic encephalopathy. Ethylmalonic acid is identified in the urine of patients with short-chain acyl-coenzyme A dehydrogenase deficiency, which is a fatty acid metabolism disorder. When present in sufficiently high levels, ethylmalonic acid can act as an acidogen and a metabotoxin. An acidogen is an acidic compound that induces acidosis, which has multiple adverse effects on many organ systems. A metabotoxin is an endogenously produced metabolite that causes adverse health effects at chronically high levels. Ethylmalonic acid is an organic acid. Abnormally high levels of organic acids in the blood (organic acidemia), urine (organic aciduria), the brain, and other tissues lead to general metabolic acidosis. Acidosis typically occurs when arterial pH falls below 7.35. In infants with acidosis, the initial symptoms include poor feeding, vomiting, loss of appetite, weak muscle tone (hypotonia), and lack of energy (lethargy). These can progress to heart abnormalities, kidney abnormalities, liver damage, seizures, coma, and possibly death. These are also the characteristic symptoms of the untreated IEMs mentioned above. Many affected children with organic acidemias experience intellectual disability or delayed development. In adults, acidosis or acidemia is characterized by headaches, confusion, feeling tired, tremors, sleepiness, and seizures.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0001309 (Ethylmalonic acid)


  Mrv1652303162022072D          

  9  8  0  0  0  0            999 V2000
   -0.7145    0.4124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2374    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    1.2374    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  1  4  2  0  0  0  0
  1  5  1  0  0  0  0
  3  6  2  0  0  0  0
  3  7  1  0  0  0  0
  8  9  1  0  0  0  0
  2  8  1  0  0  0  0
M  END
Download

3D MOL for NP0001309 (Ethylmalonic acid)

HMDB0000622
     RDKit          3D
Ethylmalonic acid
 17 16  0  0  0  0  0  0  0  0999 V2000
    2.1034    0.5785   -0.1623 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0448   -0.4024   -0.6041 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2054   -0.2623    0.2054 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2096   -1.2478   -0.2701 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9427   -2.0303   -1.2147 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4609   -1.3146    0.3280 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8060    1.0639    0.1557 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2743    1.9697   -0.5248 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9611    1.3573    0.8464 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1067    0.1303   -0.3583 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9682    0.8067    0.9152 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0024    1.4958   -0.7609 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4628   -1.4254   -0.3790 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8867   -0.3659   -1.6912 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0802   -0.4941    1.2735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6129   -2.0834    0.9654 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1824    2.2241    1.2758 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
  3  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  0
  2 14  1  0
  3 15  1  0
  6 16  1  0
  9 17  1  0
M  END
Download

3D SDF for NP0001309 (Ethylmalonic acid)


  Mrv1652303162022072D          

  9  8  0  0  0  0            999 V2000
   -0.7145    0.4124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2374    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    1.2374    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  1  4  2  0  0  0  0
  1  5  1  0  0  0  0
  3  6  2  0  0  0  0
  3  7  1  0  0  0  0
  8  9  1  0  0  0  0
  2  8  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0001309

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC(C(O)=O)C(O)=O

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

> <INCHI_KEY>
UKFXDFUAPNAMPJ-UHFFFAOYSA-N

> <FORMULA>
C5H8O4

> <MOLECULAR_WEIGHT>
132.1146

> <EXACT_MASS>
132.042258744

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
11.976514317112754

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-ethylpropanedioic acid

> <ALOGPS_LOGP>
0.43

> <JCHEM_LOGP>
0.6564376749999998

> <ALOGPS_LOGS>
-0.15

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.580590600104313

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.495963643151088

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
28.1633

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.41e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ethylmalonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0001309 (Ethylmalonic acid)

HMDB0000622
     RDKit          3D
Ethylmalonic acid
 17 16  0  0  0  0  0  0  0  0999 V2000
    2.1034    0.5785   -0.1623 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0448   -0.4024   -0.6041 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2054   -0.2623    0.2054 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2096   -1.2478   -0.2701 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9427   -2.0303   -1.2147 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4609   -1.3146    0.3280 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8060    1.0639    0.1557 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2743    1.9697   -0.5248 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9611    1.3573    0.8464 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1067    0.1303   -0.3583 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9682    0.8067    0.9152 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0024    1.4958   -0.7609 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4628   -1.4254   -0.3790 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8867   -0.3659   -1.6912 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0802   -0.4941    1.2735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6129   -2.0834    0.9654 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1824    2.2241    1.2758 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
  3  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  0
  2 14  1  0
  3 15  1  0
  6 16  1  0
  9 17  1  0
M  END
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PDB for NP0001309 (Ethylmalonic acid)

HEADER    PROTEIN                                 16-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-MAR-20         0                                  
HETATM    1  C   UNK     0      -1.334   0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   0.770   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.000  -1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
CONECT    1    2    4    5                                                  
CONECT    2    1    3    8                                                  
CONECT    3    2    6    7                                                  
CONECT    4    1                                                            
CONECT    5    1                                                            
CONECT    6    3                                                            
CONECT    7    3                                                            
CONECT    8    9    2                                                       
CONECT    9    8                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for NP0001309 (Ethylmalonic acid)

COMPND    HMDB0000622
HETATM    1  C1  UNL     1       2.103   0.579  -0.162  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.045  -0.402  -0.604  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.205  -0.262   0.205  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.210  -1.248  -0.270  1.00  0.00           C  
HETATM    5  O1  UNL     1      -0.943  -2.030  -1.215  1.00  0.00           O  
HETATM    6  O2  UNL     1      -2.461  -1.315   0.328  1.00  0.00           O  
HETATM    7  C5  UNL     1      -0.806   1.064   0.156  1.00  0.00           C  
HETATM    8  O3  UNL     1      -0.274   1.970  -0.525  1.00  0.00           O  
HETATM    9  O4  UNL     1      -1.961   1.357   0.846  1.00  0.00           O  
HETATM   10  H1  UNL     1       3.107   0.130  -0.358  1.00  0.00           H  
HETATM   11  H2  UNL     1       1.968   0.807   0.915  1.00  0.00           H  
HETATM   12  H3  UNL     1       2.002   1.496  -0.761  1.00  0.00           H  
HETATM   13  H4  UNL     1       1.463  -1.425  -0.379  1.00  0.00           H  
HETATM   14  H5  UNL     1       0.887  -0.366  -1.691  1.00  0.00           H  
HETATM   15  H6  UNL     1       0.080  -0.494   1.273  1.00  0.00           H  
HETATM   16  H7  UNL     1      -2.613  -2.083   0.965  1.00  0.00           H  
HETATM   17  H8  UNL     1      -2.182   2.224   1.276  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3   13   14
CONECT    3    4    7   15
CONECT    4    5    5    6
CONECT    6   16
CONECT    7    8    8    9
CONECT    9   17
END
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SMILES for NP0001309 (Ethylmalonic acid)

CCC(C(O)=O)C(O)=O
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INCHI for NP0001309 (Ethylmalonic acid)

InChI=1S/C5H8O4/c1-2-3(4(6)7)5(8)9/h3H,2H2,1H3,(H,6,7)(H,8,9)
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View in JSmol
Synonyms
ValueSource
1,1-Propanedicarboxylic acidChEBI
2-Ethylmalonic acidChEBI
alpha-Carboxybutyric acidChEBI
1,1-PropanedicarboxylateGenerator
2-EthylmalonateGenerator
a-CarboxybutyrateGenerator
a-Carboxybutyric acidGenerator
alpha-CarboxybutyrateGenerator
Α-carboxybutyrateGenerator
Α-carboxybutyric acidGenerator
EthylmalonateGenerator
Ethyl-malonic acidHMDB
2-Ethylpropanedioic acidHMDB
Ethylmalonic acidHMDB
Chemical FormulaC5H8O4
Average Mass132.1146 Da
Monoisotopic Mass132.04226 Da
IUPAC Name2-ethylpropanedioic acid
Traditional Nameethylmalonic acid
CAS Registry Number601-75-2
SMILES
CCC(C(O)=O)C(O)=O
InChI Identifier
InChI=1S/C5H8O4/c1-2-3(4(6)7)5(8)9/h3H,2H2,1H3,(H,6,7)(H,8,9)
InChI KeyUKFXDFUAPNAMPJ-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
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 branched fatty acids. These are fatty acids containing a branched chain.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentBranched fatty acids
Alternative Parents
Substituents
  • Branched fatty acid
  • 1,3-dicarbonyl compound
  • 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 Point112 - 114 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility712 mg/mLNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility94.1 g/LALOGPS
logP0.43ALOGPS
logP0.66ChemAxon
logS-0.15ALOGPS
pKa (Strongest Acidic)2.5ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity28.16 m³·mol⁻¹ChemAxon
Polarizability11.98 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000622
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022147
KNApSAcK IDC00052274
Chemspider ID11263
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID4180
PubChem Compound11756
PDB IDNot Available
ChEBI ID741548
Good Scents IDrw1246381
References
General References
  1. Tiranti V, D'Adamo P, Briem E, Ferrari G, Mineri R, Lamantea E, Mandel H, Balestri P, Garcia-Silva MT, Vollmer B, Rinaldo P, Hahn SH, Leonard J, Rahman S, Dionisi-Vici C, Garavaglia B, Gasparini P, Zeviani M: Ethylmalonic encephalopathy is caused by mutations in ETHE1, a gene encoding a mitochondrial matrix protein. Am J Hum Genet. 2004 Feb;74(2):239-52. Epub 2004 Jan 19. [PubMed:14732903 ]
  2. McGowan KA, Nyhan WL, Barshop BA, Naviaux RK, Yu A, Haas RH, Townsend JJ: The role of methionine in ethylmalonic encephalopathy with petechiae. Arch Neurol. 2004 Apr;61(4):570-4. [PubMed:15096407 ]
  3. Birkebaek NH, Simonsen H, Gregersen N: Hypoglycaemia and elevated urine ethylmalonic acid in a child homozygous for the short-chain acyl-CoA dehydrogenase 625G > A gene variation. Acta Paediatr. 2002;91(4):480-2. [PubMed:12061367 ]
  4. Tanaka K, Ramsdell HS, Baretz BH, Keefe MB, Kean EA, Johnson B: Identification of ethylmalonic acid in urine of two patients with the vomitting sickness of Jamaica. Clin Chim Acta. 1976 May 17;69(1):105-12. [PubMed:1269146 ]
  5. 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 ]
  6. Bok LA, Vreken P, Wijburg FA, Wanders RJ, Gregersen N, Corydon MJ, Waterham HR, Duran M: Short-chain Acyl-CoA dehydrogenase deficiency: studies in a large family adding to the complexity of the disorder. Pediatrics. 2003 Nov;112(5):1152-5. [PubMed:14595061 ]
  7. Barschak AG, Ferreira Gda C, Andre KR, Schuck PF, Viegas CM, Tonin A, Dutra Filho CS, Wyse AT, Wannmacher CM, Vargas CR, Wajner M: Inhibition of the electron transport chain and creatine kinase activity by ethylmalonic acid in human skeletal muscle. Metab Brain Dis. 2006 Mar;21(1):11-9. Epub 2006 Apr 28. [PubMed:16773466 ]