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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2021-01-04 21:28:42 UTC
HMDB IDHMDB0001147
Secondary Accession Numbers
  • HMDB01147
Metabolite Identification
Common NameAminomalonic acid
DescriptionAminomalonic acid (Ama) is an amino dicarboxylic acid that is an analog of malonic acid in which one of the methylene hydrogens has been replaced by an amino group. It is a strongly acidic compound that is very water soluble. Aminomalonic acid is a natural occurring, largely non-proteogenic amino acid that was first detected in alkaline hydrolysates of proteins in 1984. In particular, aminomalonic acid was isolated from proteins isolated from Escherichia coli cultures and from human atherosclerotic plaques (PMID: 6366787 ). Aminomalonic acid is a relatively unstable, minor amino acid in complex structures such as bacteria or tissues. The presence of aminomalonic acid has important biological implications because the malonic acid moiety potentially imparts calcium binding properties to proteins. Possible origins of aminomalonic acid in proteins include its introduction via errors in protein synthesis and oxidative damage to amino acid residues in proteins. (PMID: 1621954 , 6366787  ). Aminomalonic acid can be generated naturally via the activity of mammalian and bacterial enzymes on various precursors such as 2-aminomalonamide, diethylaminomalonate and ketomalonic acid (PMID: 35346 ). Free aminomalonic acid appears to be an oxidation product arising from perturbed serine or threonine metabolism. Aminomalonic acid is produced in animals that have been exposed to Cadmium (a strong pro-oxidant) for extended periods of time and it has been proposed to be a potential biomarker of Cadmium toxicity (PMID: 32193438 ). Aminomalonic acid has also been found to be elevated in the urine of individuals with anxiety and major depressive disorders (PMID: 30232320 ). Aminomalonic acid has been reported to be a potential biomarker for hepatocellular carcinoma (PMID: 18767022 ) and it exhibits strong inhibitory effects on L-asparagine synthase (PMID: 35346 ). Several metabolomics studies have also found that altered aminomalonic acid levels in serum are associated with neuropsychiatric disorders, melanoma, ketamine overdose and aortic aneurysm, indicating that aminomalonic acid is an important serum indicator for diseases and toxicities (PMID: 32193438 ).
Structure
Data?1582752180
Synonyms
ValueSource
2-Aminomalonic acidChEBI
AminomalonateChEBI
2-AminomalonateGenerator
a-Aminomalonic acidHMDB
alpha-Aminomalonic acidHMDB
amino-Malonic acidHMDB
amino-PropanedioateHMDB
amino-Propanedioic acidHMDB
AminopropanedioateHMDB
Aminopropanedioic acidHMDB
Chemical FormulaC3H5NO4
Average Molecular Weight119.0761
Monoisotopic Molecular Weight119.021857653
IUPAC Name2-aminopropanedioic acid
Traditional Nameaminomalonic acid
CAS Registry Number1068-84-4
SMILES
NC(C(O)=O)C(O)=O
InChI Identifier
InChI=1S/C3H5NO4/c4-1(2(5)6)3(7)8/h1H,4H2,(H,5,6)(H,7,8)
InChI KeyJINBYESILADKFW-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha amino acids
Alternative Parents
Substituents
  • Alpha-amino acid
  • Dicarboxylic acid or derivatives
  • 1,3-dicarbonyl compound
  • Amino acid
  • Carboxylic acid
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Organic oxygen compound
  • Carbonyl group
  • Amine
  • Organic nitrogen compound
  • Organic oxide
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Disposition

Biological location

Source

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility126 g/LALOGPS
logP-3.5ALOGPS
logP-3.4ChemAxon
logS0.03ALOGPS
pKa (Strongest Acidic)0.45ChemAxon
pKa (Strongest Basic)8.5ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area100.62 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity21.98 m³·mol⁻¹ChemAxon
Polarizability9.48 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+122.86631661259
DarkChem[M-H]-117.60731661259
AllCCS[M+H]+129.81532859911
AllCCS[M-H]-118.94332859911
DeepCCS[M+H]+119.24230932474
DeepCCS[M-H]-116.44130932474
DeepCCS[M-2H]-152.9130932474
DeepCCS[M+Na]+127.54730932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Aminomalonic acidNC(C(O)=O)C(O)=O1775.7Standard polar33892256
Aminomalonic acidNC(C(O)=O)C(O)=O1077.3Standard non polar33892256
Aminomalonic acidNC(C(O)=O)C(O)=O1908.9Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Aminomalonic acid,1TMS,isomer #1C[Si](C)(C)OC(=O)C(N)C(=O)O1257.1Semi standard non polar33892256
Aminomalonic acid,1TMS,isomer #2C[Si](C)(C)NC(C(=O)O)C(=O)O1325.4Semi standard non polar33892256
Aminomalonic acid,2TMS,isomer #1C[Si](C)(C)OC(=O)C(N)C(=O)O[Si](C)(C)C1308.9Semi standard non polar33892256
Aminomalonic acid,2TMS,isomer #2C[Si](C)(C)NC(C(=O)O)C(=O)O[Si](C)(C)C1376.8Semi standard non polar33892256
Aminomalonic acid,2TMS,isomer #3C[Si](C)(C)N(C(C(=O)O)C(=O)O)[Si](C)(C)C1549.6Semi standard non polar33892256
Aminomalonic acid,3TMS,isomer #1C[Si](C)(C)NC(C(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C1463.6Semi standard non polar33892256
Aminomalonic acid,3TMS,isomer #1C[Si](C)(C)NC(C(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C1427.9Standard non polar33892256
Aminomalonic acid,3TMS,isomer #1C[Si](C)(C)NC(C(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C1566.2Standard polar33892256
Aminomalonic acid,3TMS,isomer #2C[Si](C)(C)OC(=O)C(C(=O)O)N([Si](C)(C)C)[Si](C)(C)C1557.9Semi standard non polar33892256
Aminomalonic acid,3TMS,isomer #2C[Si](C)(C)OC(=O)C(C(=O)O)N([Si](C)(C)C)[Si](C)(C)C1460.0Standard non polar33892256
Aminomalonic acid,3TMS,isomer #2C[Si](C)(C)OC(=O)C(C(=O)O)N([Si](C)(C)C)[Si](C)(C)C1679.8Standard polar33892256
Aminomalonic acid,4TMS,isomer #1C[Si](C)(C)OC(=O)C(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C1639.0Semi standard non polar33892256
Aminomalonic acid,4TMS,isomer #1C[Si](C)(C)OC(=O)C(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C1547.6Standard non polar33892256
Aminomalonic acid,4TMS,isomer #1C[Si](C)(C)OC(=O)C(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C1543.9Standard polar33892256
Aminomalonic acid,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C(N)C(=O)O1508.4Semi standard non polar33892256
Aminomalonic acid,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)NC(C(=O)O)C(=O)O1603.4Semi standard non polar33892256
Aminomalonic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C(N)C(=O)O[Si](C)(C)C(C)(C)C1735.8Semi standard non polar33892256
Aminomalonic acid,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)NC(C(=O)O)C(=O)O[Si](C)(C)C(C)(C)C1804.6Semi standard non polar33892256
Aminomalonic acid,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)N(C(C(=O)O)C(=O)O)[Si](C)(C)C(C)(C)C1951.1Semi standard non polar33892256
Aminomalonic acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)NC(C(=O)O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2055.8Semi standard non polar33892256
Aminomalonic acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)NC(C(=O)O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2044.3Standard non polar33892256
Aminomalonic acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)NC(C(=O)O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C1996.8Standard polar33892256
Aminomalonic acid,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)C(C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2173.2Semi standard non polar33892256
Aminomalonic acid,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)C(C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2098.5Standard non polar33892256
Aminomalonic acid,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)C(C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2035.9Standard polar33892256
Aminomalonic acid,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C(C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2415.3Semi standard non polar33892256
Aminomalonic acid,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C(C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2345.1Standard non polar33892256
Aminomalonic acid,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C(C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2068.5Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - Aminomalonic acid GC-MS (2 TMS)splash10-001i-2910000000-56ddccdbe51afd85dd6c2014-06-16HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Aminomalonic acid GC-MS (3 TMS)splash10-0gb9-1790000000-1a2cf2f982d08de4d2c92014-06-16HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Aminomalonic acid GC-MS (Non-derivatized)splash10-001i-2910000000-56ddccdbe51afd85dd6c2017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Aminomalonic acid GC-MS (Non-derivatized)splash10-0gb9-1790000000-1a2cf2f982d08de4d2c92017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Aminomalonic acid GC-EI-TOF (Non-derivatized)splash10-0012-1920000000-706a1afd4a87657ef9242017-09-12HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Aminomalonic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-00xu-9200000000-a92a1873b06d13a3cb1b2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Aminomalonic acid GC-MS (2 TMS) - 70eV, Positivesplash10-006t-7910000000-820eb39fc624884c77c92017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Aminomalonic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Aminomalonic acid 20V, Positive-QTOFsplash10-05i0-9000000000-6da4c50b66acac061cd82021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Aminomalonic acid 40V, Positive-QTOFsplash10-0a4i-9000000000-081c80e5b8aaa8f7ba342021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Aminomalonic acid 10V, Positive-QTOFsplash10-00fr-9000000000-4dbbb4215703aa499e1b2021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Aminomalonic acid 10V, Positive-QTOFsplash10-00di-8900000000-ce915814c1e82c9da3e22015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Aminomalonic acid 20V, Positive-QTOFsplash10-00di-9200000000-c4dc8ccb28224391491f2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Aminomalonic acid 40V, Positive-QTOFsplash10-056r-9000000000-dda49c2194c794dfeebb2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Aminomalonic acid 10V, Negative-QTOFsplash10-014i-2900000000-b31a9403ea30555205e62015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Aminomalonic acid 20V, Negative-QTOFsplash10-01b9-5900000000-8f53ff3974857296fab82015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Aminomalonic acid 40V, Negative-QTOFsplash10-00di-9000000000-179c8f28fed467f080592015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Aminomalonic acid 10V, Positive-QTOFsplash10-00di-9200000000-2cbb45bb0d131a8a5a4c2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Aminomalonic acid 20V, Positive-QTOFsplash10-00di-9000000000-6bf2575f705bcef140f52021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Aminomalonic acid 40V, Positive-QTOFsplash10-0a4i-9000000000-1f92eb692a3016f518862021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Aminomalonic acid 10V, Negative-QTOFsplash10-014i-3900000000-2c6e9d09fa238ac1618c2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Aminomalonic acid 20V, Negative-QTOFsplash10-00di-9400000000-ce7be9ee668d87a767bd2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Aminomalonic acid 40V, Negative-QTOFsplash10-00dl-9000000000-a28af5b62f46a4285ac22021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Feces
  • Sweat
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal
details
FecesDetected but not QuantifiedNot QuantifiedInfant (0-1 year old)Both
Normal
details
SweatDetected but not QuantifiedNot QuantifiedAdult BothNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothBladder cancer details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB02289
Phenol Explorer Compound IDNot Available
FooDB IDFDB022451
KNApSAcK IDNot Available
Chemspider ID90998
KEGG Compound IDC00872
BioCyc IDAMINOMALONATE
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound100714
PDB IDNot Available
ChEBI ID17475
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceMatthew, Margaret; Neuberger, A. Aminomalonate. I.U.B. (Intern. Union Biochem.) Symp. Ser. (1963), Volume Date 1962, 30 243-51.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Copley SD, Frank E, Kirsch WM, Koch TH: Detection and possible origins of aminomalonic acid in protein hydrolysates. Anal Biochem. 1992 Feb 14;201(1):152-7. [PubMed:1621954 ]
  2. Van Buskirk JJ, Kirsch WM, Kleyer DL, Barkley RM, Koch TH: Aminomalonic acid: identification in Escherichia coli and atherosclerotic plaque. Proc Natl Acad Sci U S A. 1984 Feb;81(3):722-5. [PubMed:6366787 ]
  3. Milman HA, Muth R, Cooney DA: Aminomalonic acid and its congeners as potential in vivo inhibitors of L-asparagine synthetase. Enzyme. 1979;24(1):36-47. doi: 10.1159/000458626. [PubMed:35346 ]
  4. Xu MY, Wang P, Sun YJ, Yang L, Wu YJ: Identification of metabolite biomarkers in serum of rats exposed to chlorpyrifos and cadmium. Sci Rep. 2020 Mar 19;10(1):4999. doi: 10.1038/s41598-020-61982-4. [PubMed:32193438 ]
  5. Chen JJ, Bai SJ, Li WW, Zhou CJ, Zheng P, Fang L, Wang HY, Liu YY, Xie P: Urinary biomarker panel for diagnosing patients with depression and anxiety disorders. Transl Psychiatry. 2018 Sep 19;8(1):192. doi: 10.1038/s41398-018-0245-0. [PubMed:30232320 ]
  6. Xue R, Lin Z, Deng C, Dong L, Liu T, Wang J, Shen X: A serum metabolomic investigation on hepatocellular carcinoma patients by chemical derivatization followed by gas chromatography/mass spectrometry. Rapid Commun Mass Spectrom. 2008 Oct;22(19):3061-8. doi: 10.1002/rcm.3708. [PubMed:18767022 ]