Hmdb loader
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 14:17:36 UTC
Update Date2022-03-07 02:49:12 UTC
HMDB IDHMDB0002095
Secondary Accession Numbers
  • HMDB0062496
  • HMDB0062592
  • HMDB02095
  • HMDB62496
  • HMDB62592
Metabolite Identification
Common NameMalonylcarnitine
DescriptionMalonylcarnitine is a metabolite that accumulates with specific disruption of fatty-acid oxidation caused by the impaired entry of long-chain acylcarnitine esters into the mitochondria and failure of the mitochondrial respiratory chain at complex 11 and malonyl-CoA decarboxylase (EC 4.1.1.9) deficiency (OMIM: 248360 ). Malonylcarnitine has also been found to accumulate in some newborns with medium-chain acyl-CoA dehydrogenase (EC 1.3.99.3) deficiency (OMIM: 201450 ). (PMID:11558490 , 15303003 , 12651823 ).
Structure
Data?1582752229
Synonyms
ValueSource
Malonyl-carnitinHMDB
Malonyl-carnitineHMDB
Malonyl-L-carnitineHMDB
O-Malonyl-L-carnitineHMDB
O-MalonylcarnitineHMDB
MalonylcarnitineHMDB
Chemical FormulaC10H17NO6
Average Molecular Weight247.247
Monoisotopic Molecular Weight247.105587271
IUPAC Name(3R)-3-[(2-carboxyacetyl)oxy]-4-(trimethylazaniumyl)butanoate
Traditional Name(3R)-3-[(2-carboxyacetyl)oxy]-4-(trimethylammonio)butanoate
CAS Registry Number910825-21-7
SMILES
C[N+](C)(C)C[C@@H](CC([O-])=O)OC(=O)CC(O)=O
InChI Identifier
InChI=1S/C10H17NO6/c1-11(2,3)6-7(4-8(12)13)17-10(16)5-9(14)15/h7H,4-6H2,1-3H3,(H-,12,13,14,15)/t7-/m1/s1
InChI KeyZGNBLKBZJBJFDG-SSDOTTSWSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as acyl carnitines. These are organic compounds containing a fatty acid with the carboxylic acid attached to carnitine through an ester bond.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acid esters
Direct ParentAcyl carnitines
Alternative Parents
Substituents
  • Acyl-carnitine
  • Tricarboxylic acid or derivatives
  • 1,3-dicarbonyl compound
  • Quaternary ammonium salt
  • Tetraalkylammonium salt
  • Carboxylic acid salt
  • Carboxylic acid ester
  • Carboxylic acid
  • Carboxylic acid derivative
  • Hydrocarbon derivative
  • Organic salt
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Amine
  • Organic oxide
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
Role
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 Solubility0.34 g/LALOGPS
logP-2ALOGPS
logP-4.6ChemAxon
logS-3ALOGPS
pKa (Strongest Acidic)3.47ChemAxon
pKa (Strongest Basic)-7.2ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area103.73 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity78.98 m³·mol⁻¹ChemAxon
Polarizability23.68 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
DeepCCS[M+H]+158.36130932474
DeepCCS[M-H]-155.96630932474
DeepCCS[M-2H]-188.98430932474
DeepCCS[M+Na]+164.40130932474
AllCCS[M+H]+155.132859911
AllCCS[M+H-H2O]+152.032859911
AllCCS[M+NH4]+158.032859911
AllCCS[M+Na]+158.932859911
AllCCS[M-H]-160.932859911
AllCCS[M+Na-2H]-161.732859911
AllCCS[M+HCOO]-162.732859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
MalonylcarnitineC[N+](C)(C)C[C@@H](CC([O-])=O)OC(=O)CC(O)=O2841.1Standard polar33892256
MalonylcarnitineC[N+](C)(C)C[C@@H](CC([O-])=O)OC(=O)CC(O)=O1311.1Standard non polar33892256
MalonylcarnitineC[N+](C)(C)C[C@@H](CC([O-])=O)OC(=O)CC(O)=O1754.7Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Malonylcarnitine,1TMS,isomer #1C[N+](C)(C)C[C@@H](CC(=O)[O-])OC(=O)CC(=O)O[Si](C)(C)C1719.2Semi standard non polar33892256
Malonylcarnitine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CC(=O)O[C@H](CC(=O)[O-])C[N+](C)(C)C1961.6Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Malonylcarnitine GC-MS (1 TMS) - 70eV, Positivesplash10-00di-9110000000-c695dab07ed816875c722017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Malonylcarnitine 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 - Malonylcarnitine LC-ESI-QQ , positive-QTOFsplash10-03di-0900000000-9b579c570aab7c7d3a212019-05-16HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Malonylcarnitine LC-ESI-QQ , positive-QTOFsplash10-0ik9-0900000000-e37d3def2de1af5bd2f52019-05-16HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Malonylcarnitine LC-ESI-QQ , positive-QTOFsplash10-0ue9-8900000000-cf37f0a721cd52d86e8e2019-05-16HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Malonylcarnitine LC-ESI-QQ , positive-QTOFsplash10-0r0c-9200000000-a11a4872036f3c33d25a2019-05-16HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Malonylcarnitine LC-ESI-QQ , positive-QTOFsplash10-0a4l-9000000000-2402e260a330ff1772a12019-05-16HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Malonylcarnitine LC-ESI-IT , positive-QTOFsplash10-0w29-6900000000-d0136248acdd706e650b2019-05-16HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Malonylcarnitine LC-ESI-QTOF , positive-QTOFsplash10-0ik9-2900000000-61732bb10307f2b183ca2019-05-16HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Malonylcarnitine LC-ESI-QTOF , positive-QTOFsplash10-0zg0-9400000000-15c3db3324f1d46d3c7c2019-05-16HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Malonylcarnitine LC-ESI-QTOF , positive-QTOFsplash10-0ik9-2900000000-ee79f10dce9fc09246ec2019-05-16HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Malonylcarnitine 10V, Positive-QTOFsplash10-0002-0090000000-76e7a2e41e371aa253262021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Malonylcarnitine 20V, Positive-QTOFsplash10-000j-9050000000-ca80627c48799e4dbe5f2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Malonylcarnitine 40V, Positive-QTOFsplash10-000i-9000000000-e9262cbaff8cb4ad0ba62021-09-22Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen Locations
  • Blood
  • Urine
Tissue Locations
  • Placenta
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.030-0.090 uMAdult (>18 years old)Both
Normal
details
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.1 (0 - 0.2) uMChildren (1-13 years old)Not SpecifiedNormal details
BloodDetected and Quantified<0.30 uMNewborn (0-30 days old)BothNormal details
UrineDetected and Quantified0.02 (0.01-0.04) umol/mmol creatinineAdult (>18 years old)Both
Normal
details
UrineDetected and Quantified0.01-0.08 umol/mmol creatinineNewborn (0-30 days old)BothNormal details
UrineDetected and Quantified0.04 +/- 0.02 umol/mmol creatinineNewborn (0-30 days old)FemaleNormal details
UrineDetected and Quantified0.04 +/- 0.02 umol/mmol creatinineNewborn (0-30 days old)MaleNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified2.7 (1.6 - 3.8) uMNewborn (0-30 days old)Not SpecifiedMalonyl-CoA decarboxylase deficiency details
BloodDetected and Quantified0.2 (0.13 - 0.3) uMInfant (0-1 year old)Not SpecifiedMalonyl-CoA decarboxylase deficiency details
BloodDetected and Quantified46.8 (24.8) uMAdult (>18 years old)FemaleLate-onset preeclampsia details
BloodDetected and Quantified27.8 (20.0) uMAdult (>18 years old)FemalePregnancy details
BloodDetected and Quantified50.65(14.14) uMAdult (>18 years old)BothHeart failure with preserved ejection fraction details
Associated Disorders and Diseases
Disease References
Malonyl-Coa decarboxylase deficiency
  1. Santer R, Fingerhut R, Lassker U, Wightman PJ, Fitzpatrick DR, Olgemoller B, Roscher AA: Tandem mass spectrometric determination of malonylcarnitine: diagnosis and neonatal screening of malonyl-CoA decarboxylase deficiency. Clin Chem. 2003 Apr;49(4):660-2. [PubMed:12651823 ]
  2. Ficicioglu C, Chrisant MR, Payan I, Chace DH: Cardiomyopathy and hypotonia in a 5-month-old infant with malonyl-coa decarboxylase deficiency: potential for preclinical diagnosis with expanded newborn screening. Pediatr Cardiol. 2005 Nov-Dec;26(6):881-3. [PubMed:16078122 ]
Late-onset preeclampsia
  1. Bahado-Singh RO, Akolekar R, Mandal R, Dong E, Xia J, Kruger M, Wishart DS, Nicolaides K: First-trimester metabolomic detection of late-onset preeclampsia. Am J Obstet Gynecol. 2013 Jan;208(1):58.e1-7. doi: 10.1016/j.ajog.2012.11.003. Epub 2012 Nov 13. [PubMed:23159745 ]
Pregnancy
  1. Bahado-Singh RO, Akolekar R, Mandal R, Dong E, Xia J, Kruger M, Wishart DS, Nicolaides K: First-trimester metabolomic detection of late-onset preeclampsia. Am J Obstet Gynecol. 2013 Jan;208(1):58.e1-7. doi: 10.1016/j.ajog.2012.11.003. Epub 2012 Nov 13. [PubMed:23159745 ]
Associated OMIM IDs
  • 248360 (Malonyl-Coa decarboxylase deficiency)
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022843
KNApSAcK IDNot Available
Chemspider ID34999703
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID6484
PubChem Compound91825606
PDB IDNot Available
ChEBI ID85470
Food Biomarker OntologyNot Available
VMH IDHC10859
MarkerDB IDMDB00000376
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Johnson DW, Trinh MU: Stability of malonylcarnitine and glutarylcarnitine in stored blood spots. J Inherit Metab Dis. 2004;27(6):789-90. [PubMed:15617193 ]
  2. Santer R, Fingerhut R, Lassker U, Wightman PJ, Fitzpatrick DR, Olgemoller B, Roscher AA: Tandem mass spectrometric determination of malonylcarnitine: diagnosis and neonatal screening of malonyl-CoA decarboxylase deficiency. Clin Chem. 2003 Apr;49(4):660-2. [PubMed:12651823 ]
  3. Napolitano N, Wiley V, Pitt JJ: Pseudo-glutarylcarnitinaemia in medium-chain acyl-CoA dehydrogenase deficiency detected by tandem mass spectrometry newborn screening. J Inherit Metab Dis. 2004;27(4):465-71. [PubMed:15303003 ]
  4. Wolf A, Weir P, Segar P, Stone J, Shield J: Impaired fatty acid oxidation in propofol infusion syndrome. Lancet. 2001 Feb 24;357(9256):606-7. [PubMed:11558490 ]
  5. Ficicioglu C, Chrisant MR, Payan I, Chace DH: Cardiomyopathy and hypotonia in a 5-month-old infant with malonyl-coa decarboxylase deficiency: potential for preclinical diagnosis with expanded newborn screening. Pediatr Cardiol. 2005 Nov-Dec;26(6):881-3. [PubMed:16078122 ]
  6. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  7. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  8. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  9. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  10. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]
  11. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.