Hmdb loader
You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2009-04-06 16:20:07 UTC
Update Date2020-02-26 21:37:00 UTC
HMDB IDHMDB0012154
Secondary Accession Numbers
  • HMDB12154
Metabolite Identification
Common Name3-Dehydrocarnitine
Description3-Dehydrocarnitine is a member of the carnitine family that is an intermediate in carnitine degradation. It can be formed from either D-carnitine or L-carnitine and the enzyme responsible for this oxidation reaction is (S)-carnitine 3-dehydrogenase (EC 1.1.1.254) or carnitine 3-dehydrogenase (EC 1.1.1.108), respectively. Carnitine is a quaternary ammonium compound biosynthesized from the amino acids lysine and methionine. In living cells, it is required for the transport of fatty acids from the cytosol into the mitochondria during the breakdown of lipids (or fats) for the generation of metabolic energy.
Structure
Data?1582753020
Synonyms
ValueSource
3-oxo-4-(Trimethylammonio)butanoateChEBI
3-oxo-4-(Trimethylammonio)butanoic acidGenerator
3-Carboxy-N,N,N-trimethyl-2-oxo-1-propanaminiumHMDB
3-Carboxy-N,N,N-trimethyl-2-oxopropan-1-aminiumHMDB
Chemical FormulaC7H13NO3
Average Molecular Weight159.183
Monoisotopic Molecular Weight159.089543287
IUPAC Name3-oxo-4-(trimethylazaniumyl)butanoate
Traditional Name3-dehydrocarnitine
CAS Registry Number10457-99-5
SMILES
C[N+](C)(C)CC(=O)CC([O-])=O
InChI Identifier
InChI=1S/C7H13NO3/c1-8(2,3)5-6(9)4-7(10)11/h4-5H2,1-3H3
InChI KeyYNOWULSFLVIUDH-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as short-chain keto acids and derivatives. These are keto acids with an alkyl chain the contains less than 6 carbon atoms.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassKeto acids and derivatives
Sub ClassShort-chain keto acids and derivatives
Direct ParentShort-chain keto acids and derivatives
Alternative Parents
Substituents
  • Beta-keto acid
  • Short-chain keto acid
  • 1,3-dicarbonyl compound
  • Alpha-aminoketone
  • Tetraalkylammonium salt
  • Quaternary ammonium salt
  • Carboxylic acid salt
  • Ketone
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Organic nitrogen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Organic salt
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Carbonyl group
  • Organic oxygen compound
  • Amine
  • 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 Solubility1.04 g/LALOGPS
logP-2.2ALOGPS
logP-4.3ChemAxon
logS-2.3ALOGPS
pKa (Strongest Acidic)3.94ChemAxon
pKa (Strongest Basic)-8.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area57.2 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity62.72 m³·mol⁻¹ChemAxon
Polarizability16.08 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]+130.80130932474
DeepCCS[M-H]-127.17330932474
DeepCCS[M-2H]-163.98830932474
DeepCCS[M+Na]+139.41730932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-DehydrocarnitineC[N+](C)(C)CC(=O)CC([O-])=O1722.6Standard polar33892256
3-DehydrocarnitineC[N+](C)(C)CC(=O)CC([O-])=O876.8Standard non polar33892256
3-DehydrocarnitineC[N+](C)(C)CC(=O)CC([O-])=O1206.6Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
3-Dehydrocarnitine,1TMS,isomer #1C[N+](C)(C)CC(=CC(=O)[O-])O[Si](C)(C)C1348.6Semi standard non polar33892256
3-Dehydrocarnitine,1TMS,isomer #1C[N+](C)(C)CC(=CC(=O)[O-])O[Si](C)(C)C1273.0Standard non polar33892256
3-Dehydrocarnitine,1TMS,isomer #1C[N+](C)(C)CC(=CC(=O)[O-])O[Si](C)(C)C1560.0Standard polar33892256
3-Dehydrocarnitine,1TMS,isomer #2C[N+](C)(C)C=C(CC(=O)[O-])O[Si](C)(C)C1314.7Semi standard non polar33892256
3-Dehydrocarnitine,1TMS,isomer #2C[N+](C)(C)C=C(CC(=O)[O-])O[Si](C)(C)C1318.0Standard non polar33892256
3-Dehydrocarnitine,1TMS,isomer #2C[N+](C)(C)C=C(CC(=O)[O-])O[Si](C)(C)C1497.0Standard polar33892256
3-Dehydrocarnitine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=CC(=O)[O-])C[N+](C)(C)C1567.3Semi standard non polar33892256
3-Dehydrocarnitine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=CC(=O)[O-])C[N+](C)(C)C1478.7Standard non polar33892256
3-Dehydrocarnitine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=CC(=O)[O-])C[N+](C)(C)C1680.2Standard polar33892256
3-Dehydrocarnitine,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=C[N+](C)(C)C)CC(=O)[O-]1532.6Semi standard non polar33892256
3-Dehydrocarnitine,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=C[N+](C)(C)C)CC(=O)[O-]1534.2Standard non polar33892256
3-Dehydrocarnitine,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=C[N+](C)(C)C)CC(=O)[O-]1629.3Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3-Dehydrocarnitine GC-MS (Non-derivatized) - 70eV, Positivesplash10-00di-9100000000-48a9f09b18771a5842132017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Dehydrocarnitine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Dehydrocarnitine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Dehydrocarnitine 10V, Positive-QTOFsplash10-03dl-0900000000-aeb6eb576f6ef1b5e0dc2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Dehydrocarnitine 20V, Positive-QTOFsplash10-01ox-0900000000-8132a40779df66d881952017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Dehydrocarnitine 40V, Positive-QTOFsplash10-00dj-9000000000-fa4cb3f532a0edad13952017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Dehydrocarnitine 10V, Negative-QTOFsplash10-0a4i-1900000000-968fad178ea0d8d3323e2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Dehydrocarnitine 20V, Negative-QTOFsplash10-0a4i-3900000000-3f73132f1b1134a297cb2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Dehydrocarnitine 40V, Negative-QTOFsplash10-0536-9000000000-1d039ed9a3579485a2822017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Dehydrocarnitine 10V, Negative-QTOFsplash10-0a4i-0900000000-bae995f985c28e19f14c2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Dehydrocarnitine 20V, Negative-QTOFsplash10-0a4i-9600000000-64c4aa2c4cea1dbe3c722021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Dehydrocarnitine 40V, Negative-QTOFsplash10-0a4i-9000000000-7ab6b27ea9f8d124cbe42021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Dehydrocarnitine 10V, Positive-QTOFsplash10-03di-5900000000-d4dcf40de75bf11edc512021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Dehydrocarnitine 20V, Positive-QTOFsplash10-0f7x-9100000000-38d8bba838a4cc9566332021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Dehydrocarnitine 40V, Positive-QTOFsplash10-0006-9000000000-213cfc2d6d3e2baa50e02021-09-24Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Feces
  • Saliva
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedInfant (0-1 year old)Not Specified
Normal
details
FecesDetected but not QuantifiedNot QuantifiedInfant (0-1 year old)Not Specified
Normal
details
FecesDetected but not QuantifiedNot QuantifiedInfant (0-1 year old)Not AvailableNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer
details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal adenoma
details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
  2. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
  3. Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB028811
KNApSAcK IDNot Available
Chemspider ID5360148
KEGG Compound IDC02636
BioCyc ID3-DE-H-CARNITINE
BiGG IDNot Available
Wikipedia Link3-Dehydrocarnitine
METLIN IDNot Available
PubChem Compound6991982
PDB IDNot Available
ChEBI ID57885
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available