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Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2016-06-10 21:22:53 UTC
HMDB IDHMDB00691
Secondary Accession NumbersNone
Metabolite Identification
Common NameMalonic acid
DescriptionMalonic acid (IUPAC systematic name: propanedioic acid) is a dicarboxylic acid with structure CH2(COOH)2. The ionised form of malonic acid, as well as its esters and salts, are known as malonates. For example, diethyl malonate is malonic acid's ethyl ester. The name originates from Latin malum, meaning apple. Malonic acid is the archetypal example of a competitive inhibitor: it acts against succinate dehydrogenase (complex II) in the respiratory electron transport chain.
Structure
Thumb
Synonyms
ValueSource
alpha,Omega-dicarboxylic acidHMDB
Carboxyacetic acidHMDB
DicarboxylateHMDB
Dicarboxylic acidHMDB
DicarboxymethaneHMDB
Kyselina malonovaHMDB
MalonateHMDB
Malonate dicarboxylic acidHMDB
Metahnedicarboxylic acidHMDB
Methanedicarbonic acidHMDB
Methanedicarboxylic acidHMDB
PropanedioateHMDB
Propanedioic acidHMDB
Propanedioic acid dithallium saltHMDB
Propanediolic acidHMDB
Thallium malonateHMDB
Chemical FormulaC3H4O4
Average Molecular Weight104.0615
Monoisotopic Molecular Weight104.010958616
IUPAC Namepropanedioic acid
Traditional Namemalonic acid
CAS Registry Number141-82-2
SMILES
OC(=O)CC(O)=O
InChI Identifier
InChI=1S/C3H4O4/c4-2(5)1-3(6)7/h1H2,(H,4,5)(H,6,7)
InChI KeyInChIKey=OFOBLEOULBTSOW-UHFFFAOYSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as dicarboxylic acids and derivatives. These are organic compounds containing exactly two carboxylic acid groups.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassDicarboxylic acids and derivatives
Direct ParentDicarboxylic acids and derivatives
Alternative Parents
Substituents
  • 1,3-dicarbonyl compound
  • Dicarboxylic acid or derivatives
  • Carboxylic acid
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
StatusDetected and Quantified
Origin
  • Drug metabolite
  • Endogenous
Biofunction
  • Waste products
ApplicationNot Available
Cellular locations
  • Cytoplasm (predicted from logP)
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point135 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility763.0 mg/mLNot Available
LogP-0.81HANSCH,C ET AL. (1995)
Predicted Properties
PropertyValueSource
Water Solubility197.0 mg/mLALOGPS
logP-0.6ALOGPS
logP-0.33ChemAxon
logS0.28ALOGPS
pKa (Strongest Acidic)2.43ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 Å2ChemAxon
Rotatable Bond Count2ChemAxon
Refractivity18.99 m3·mol-1ChemAxon
Polarizability8.13 Å3ChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (2 TMS)splash10-0002-1900000000-a1463432c138c328557dView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)splash10-0002-0900000000-5e58241137fee0ccc64aView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (2 TMS)splash10-006t-9700000000-54976b3ce8f36ce0676dView in MoNA
GC-MSGC-MS Spectrum - GC-MS (2 TMS)splash10-001i-4930000000-e7dbed4919870db8dabfView in MoNA
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-05gl-1943000000-456e387fdf365bf0f8eeView in MoNA
GC-MSGC-MS Spectrum - GC-MSNot Available
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Negative (Annotated)splash10-0a4i-9100000000-c7a1704f8a38ca2d245aView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Negative (Annotated)splash10-0a4l-9100000000-9fa84f43f2e19b56035cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Negative (Annotated)splash10-052f-9100000000-8a21753b343cf5dabdcbView in MoNA
LC-MS/MSLC-MS/MS Spectrum - EI-B (Unknown) , Positivesplash10-0006-9000000000-6c56a402111059603ba4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - EI-B (HITACHI RMU-7M) , Positivesplash10-0006-9000000000-f239df8fdd12e9a74445View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-0udi-3900000000-e0a4c7e792cfd0e60cc3View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-0a4i-9000000000-4c03aa889e6a98ab532fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-0a4l-9000000000-b3d14c986f292bdcf477View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-0006-9000000000-8e1041322f9acda4088aView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0006-9000000000-af4dccf21d68110099a1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
MSMass Spectrum (Electron Ionization)splash10-01ox-9000000000-dd4efef191376724d0f1View in MoNA
1D NMR13C NMR SpectrumNot Available
1D NMR1H NMR SpectrumNot Available
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biofluid Locations
  • Blood
  • Feces
  • Saliva
  • Urine
Tissue Location
  • Kidney
  • Liver
Pathways
NameSMPDB LinkKEGG Link
Aspartate MetabolismSMP00067map00250
Fatty Acid BiosynthesisSMP00456Not Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified15.0+/- 0.58 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified4.98 +/- 0.31 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified13.5 +/- 1.2 uMAdult (>18 years old)BothNormal details
FecesDetected but not QuantifiedNot ApplicableAdult (>18 years old)Both
Normal
details
FecesDetected but not QuantifiedNot ApplicableAdult (>18 years old)Both
Normal
details
FecesDetected but not QuantifiedNot ApplicableNot SpecifiedNot Specified
Normal
details
FecesDetected but not QuantifiedNot ApplicableAdult (>18 years old)Both
Normal
details
SalivaDetected and Quantified0.865 +/- 0.291 uMAdult (>18 years old)Male
Normal
    • Sugimoto et al. (...
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Both
Normal
    • Zerihun T. Dame, ...
details
SalivaDetected and Quantified0.369 +/- 0.217 uMAdult (>18 years old)Female
Normal
    • Sugimoto et al. (...
details
SalivaDetected and Quantified0.396 +/- 0.159 uMAdult (>18 years old)Female
Normal
    • Sugimoto et al. (...
details
SalivaDetected and Quantified0.504 +/- 0.177 uMAdult (>18 years old)Female
Normal
    • Sugimoto et al. (...
details
UrineDetected and Quantified13.366 +/- 10.276 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Normal
    • Mordechai, Hien, ...
details
UrineDetected and Quantified2.9 (2.0-3.5) umol/mmol creatinineAdult (>18 years old)Both
Normal
details
UrineDetected and Quantified0.8-1.5 umol/mmol creatinineAdult (>18 years old)FemaleNormal details
UrineDetected but not QuantifiedNot ApplicableAdult (>18 years old)Both
Normal
details
UrineDetected and Quantified0.8-1.1 umol/mmol creatinineAdult (>18 years old)MaleNormal details
UrineDetected and Quantified15.041 +/- 13.798 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Normal
    • Mordechai, Hien, ...
details
UrineDetected and Quantified0.6 umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified2.3 (1.2-3.1) umol/mmol creatinineAdult (>18 years old)Both
Normal
details
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified105.7 +/- 95.8 uMAdult (>18 years old)BothHeart Transplant details
UrineDetected and Quantified54.96 +/- 113.059 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Eosinophilic esophagitis
    • Mordechai, Hien, ...
details
UrineDetected and Quantified58.315 +/- 82.251 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Eosinophilic esophagitis
    • Mordechai, Hien, ...
details
UrineDetected and Quantified23.34 +/- 19.038 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Gastroesophageal reflux disease
    • Mordechai, Hien, ...
details
UrineDetected and Quantified1.0 (0.0-2.0) umol/mmol creatinineAdult (>18 years old)BothMalonyl-Coa decarboxylase deficiency details
UrineDetected and Quantified240.00 (40.00-440.00) umol/mmol creatinineChildren (1-13 years old)BothMalonyl-CoA decarboxylase deficiency details
Associated Disorders and Diseases
Disease References
Malonyl-Coa decarboxylase deficiency
  1. MetaGene [Link]
Associated OMIM IDs
  • 248360 (Malonyl-Coa decarboxylase deficiency)
DrugBank IDDB02175
DrugBank Metabolite IDDBMET00505
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB008117
KNApSAcK IDC00001193
Chemspider ID844
KEGG Compound IDC00383
BioCyc IDMALONATE
BiGG IDNot Available
Wikipedia LinkMalonic acid
NuGOwiki LinkHMDB00691
Metagene LinkHMDB00691
METLIN ID3237
PubChem Compound867
PDB IDMLA
ChEBI ID30794
References
Synthesis ReferenceBehr, Arno; Botulinski, Andreas; Carduck, Franz Josef; Schneider, Michael. Process for preparation of malonic acid. Ger. Offen. (1992), 4 pp.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Ohdoi C, Nyhan WL, Kuhara T: Chemical diagnosis of Lesch-Nyhan syndrome using gas chromatography-mass spectrometry detection. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Jul 15;792(1):123-30. [12829005 ]
  2. Yano S, Sweetman L, Thorburn DR, Mofidi S, Williams JC: A new case of malonyl coenzyme A decarboxylase deficiency presenting with cardiomyopathy. Eur J Pediatr. 1997 May;156(5):382-3. [9177981 ]
  3. Belgorodsky B, Fadeev L, Ittah V, Benyamini H, Zelner S, Huppert D, Kotlyar AB, Gozin M: Formation and characterization of stable human serum albumin-tris-malonic acid [C60]fullerene complex. Bioconjug Chem. 2005 Sep-Oct;16(5):1058-62. [16173780 ]
  4. Buyukgebiz B, Jakobs C, Scholte HR, Huijmans JG, Kleijer WJ: Fatal neonatal malonic aciduria. J Inherit Metab Dis. 1998 Feb;21(1):76-7. [9501274 ]
  5. Haan EA, Scholem RD, Croll HB, Brown GK: Malonyl coenzyme A decarboxylase deficiency. Clinical and biochemical findings in a second child with a more severe enzyme defect. Eur J Pediatr. 1986 Apr;144(6):567-70. [3709568 ]
  6. Pollitt RJ, Fowler B, Sardharwalla IB, Edwards MA, Gray RG: Increased excretion of propan-1,3-diol and 3-hydroxypropionic acid apparently caused by abnormal bacterial metabolism in the gut. Clin Chim Acta. 1987 Nov 16;169(2-3):151-7. [3427776 ]
  7. Honda A, Yamashita K, Ikegami T, Hara T, Miyazaki T, Hirayama T, Numazawa M, Matsuzaki Y: Highly-sensitive quantification of serum malonate, a possible marker for de novo lipogenesis, by LC-ESI-MS/MS. J Lipid Res. 2009 Apr 29. [19403942 ]

Enzymes

General function:
Involved in 4-aminobutyrate transaminase activity
Specific function:
Catalyzes the conversion of gamma-aminobutyrate and L-beta-aminoisobutyrate to succinate semialdehyde and methylmalonate semialdehyde, respectively. Can also convert delta-aminovalerate and beta-alanine.
Gene Name:
ABAT
Uniprot ID:
P80404
Molecular weight:
56438.405
General function:
Involved in protein kinase activity
Specific function:
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Gene Name:
SRC
Uniprot ID:
P12931
Molecular weight:
59834.3
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [17016423 ]
  3. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [10592235 ]