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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2022-03-07 02:49:07 UTC
HMDB IDHMDB0000910
Secondary Accession Numbers
  • HMDB00910
Metabolite Identification
Common NameTridecanoic acid
DescriptionTridecanoic acid, also known as N-tridecanoate or C13:0, belongs to the class of organic compounds known as long-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 13 and 21 carbon atoms. Tridecanoic acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Tridecanoic acid is a potentially toxic compound.
Structure
Data?1582752164
Synonyms
ValueSource
C13:0ChEBI
N-TRIDECANOIC ACIDChEBI
N-Tridecoic acidChEBI
Tridecylic acidChEBI
N-TRIDECANOateGenerator
N-TridecoateGenerator
TridecylateGenerator
TridecanoateGenerator
(S)-2-AminotridecanoateHMDB
(S)-2-Aminotridecanoic acidHMDB
2S-Amino-tridecanoateHMDB
2S-Amino-tridecanoic acidHMDB
Chemical FormulaC13H26O2
Average Molecular Weight214.3443
Monoisotopic Molecular Weight214.193280076
IUPAC Nametridecanoic acid
Traditional Nametridecanoic acid
CAS Registry Number638-53-9
SMILES
CCCCCCCCCCCCC(O)=O
InChI Identifier
InChI=1S/C13H26O2/c1-2-3-4-5-6-7-8-9-10-11-12-13(14)15/h2-12H2,1H3,(H,14,15)
InChI KeySZHOJFHSIKHZHA-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as long-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 13 and 21 carbon atoms.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentLong-chain fatty acids
Alternative Parents
Substituents
  • Long-chain fatty acid
  • Straight chain fatty acid
  • Monocarboxylic 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
Ontology
Physiological effect
Disposition
Biological locationRoute of exposureSource
Process
Role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point44.5 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility0.033 mg/mLNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Not Available155.163http://allccs.zhulab.cn/database/detail?ID=AllCCS00000227
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.0039 g/LALOGPS
logP5.57ALOGPS
logP4.92ChemAxon
logS-4.7ALOGPS
pKa (Strongest Acidic)4.95ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area37.3 ŲChemAxon
Rotatable Bond Count11ChemAxon
Refractivity63.28 m³·mol⁻¹ChemAxon
Polarizability27.95 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+155.3731661259
DarkChem[M-H]-153.65631661259
AllCCS[M+H]+157.4232859911
AllCCS[M-H]-158.55732859911
DeepCCS[M+H]+153.78430932474
DeepCCS[M-H]-149.7630932474
DeepCCS[M-2H]-186.9630932474
DeepCCS[M+Na]+162.70830932474
AllCCS[M+H]+157.432859911
AllCCS[M+H-H2O]+153.932859911
AllCCS[M+NH4]+160.732859911
AllCCS[M+Na]+161.632859911
AllCCS[M-H]-158.632859911
AllCCS[M+Na-2H]-159.832859911
AllCCS[M+HCOO]-161.232859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Tridecanoic acidCCCCCCCCCCCCC(O)=O2571.4Standard polar33892256
Tridecanoic acidCCCCCCCCCCCCC(O)=O1643.8Standard non polar33892256
Tridecanoic acidCCCCCCCCCCCCC(O)=O1676.7Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Tridecanoic acid,1TMS,isomer #1CCCCCCCCCCCCC(=O)O[Si](C)(C)C1748.7Semi standard non polar33892256
Tridecanoic acid,1TBDMS,isomer #1CCCCCCCCCCCCC(=O)O[Si](C)(C)C(C)(C)C1983.2Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Tridecanoic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9600000000-47009efe1dab396cbc362017-08-28Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Tridecanoic acid GC-MS (1 TMS) - 70eV, Positivesplash10-00dr-9320000000-c990904bdc703efca5ea2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Tridecanoic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Tridecanoic acid GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-06Wishart LabView Spectrum
MSMass Spectrum (Electron Ionization)splash10-06xx-9100000000-dce7696cc73940fd15692014-09-20Not AvailableView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Tridecanoic acid Quattro_QQQ 10V, N/A-QTOF (Annotated)splash10-03di-0090000000-34313db5ab452c3545d32012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Tridecanoic acid Quattro_QQQ 25V, N/A-QTOF (Annotated)splash10-03di-2190000000-d5ccc1a294cbb115ed4f2012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Tridecanoic acid ESI-TOF , Negative-QTOFsplash10-03di-0090000000-2dadd8baad50427686a72017-09-12HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Tridecanoic acid ESI-TOF 20V, Negative-QTOFsplash10-03di-0090000000-48504f2b1093306b191c2017-09-12HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Tridecanoic acid ESI-TOF 10V, Negative-QTOFsplash10-03di-0090000000-f329a7c76bcecedf8a572017-09-12HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Tridecanoic acid LC-ESI-TOF , negative-QTOFsplash10-03di-0090000000-48504f2b1093306b191c2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Tridecanoic acid LC-ESI-TOF , negative-QTOFsplash10-03di-0090000000-f329a7c76bcecedf8a572017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Tridecanoic acid 20V, Negative-QTOFsplash10-03di-0090000000-0c52e593d10a1a4101ef2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Tridecanoic acid 10V, Negative-QTOFsplash10-03di-0090000000-77f098208b1026f631232021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Tridecanoic acid 20V, Positive-QTOFsplash10-03di-0090000000-9eff77504c828cb1628c2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Tridecanoic acid 10V, Positive-QTOFsplash10-03di-0090000000-89bc5ec0a174509882b62021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Tridecanoic acid 20V, Positive-QTOFsplash10-05gm-9000000000-90d1b4c8086b81c7f9882021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Tridecanoic acid 30V, Negative-QTOFsplash10-03di-0090000000-bd44aebb2379f35e276a2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Tridecanoic acid 40V, Positive-QTOFsplash10-016r-9600000000-96a0c1cb6b605846ccef2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Tridecanoic acid 10V, Positive-QTOFsplash10-0a4r-9420000000-075a501bfd12df49789c2021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tridecanoic acid 10V, Positive-QTOFsplash10-014j-0960000000-4c8ede31869f6223161b2017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tridecanoic acid 20V, Positive-QTOFsplash10-014i-4910000000-d8d01123684b539067542017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tridecanoic acid 40V, Positive-QTOFsplash10-052f-9200000000-470003058e2f30f376702017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tridecanoic acid 10V, Negative-QTOFsplash10-03di-0290000000-5d682055384bb90ab3052017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tridecanoic acid 20V, Negative-QTOFsplash10-03xr-2790000000-eb8e86c4799f627b328a2017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tridecanoic acid 40V, Negative-QTOFsplash10-0a4i-9400000000-0c489558a9d75d20eca02017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tridecanoic acid 10V, Positive-QTOFsplash10-06dr-9210000000-f3b9b99e0fb3221d0dae2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tridecanoic acid 20V, Positive-QTOFsplash10-0avi-9000000000-a2ccb957414b847288602021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tridecanoic acid 40V, Positive-QTOFsplash10-0a4l-9000000000-af51c070c0adf27ab0c22021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tridecanoic acid 10V, Negative-QTOFsplash10-03di-0190000000-b5b304c46715ac3dfb8b2021-09-24Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Experimental 1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)2012-12-04Wishart LabView Spectrum
Experimental 2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, CDCl3, experimental)2012-12-05Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane (predicted from logP)
Biospecimen Locations
  • Feces
  • Saliva
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Not SpecifiedNormal details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothIron deficiency details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothUlcerative colitis details
Associated Disorders and Diseases
Disease References
Iron deficiency
  1. Lee T, Clavel T, Smirnov K, Schmidt A, Lagkouvardos I, Walker A, Lucio M, Michalke B, Schmitt-Kopplin P, Fedorak R, Haller D: Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with IBD. Gut. 2017 May;66(5):863-871. doi: 10.1136/gutjnl-2015-309940. Epub 2016 Feb 4. [PubMed:26848182 ]
Ulcerative colitis
  1. Lee T, Clavel T, Smirnov K, Schmidt A, Lagkouvardos I, Walker A, Lucio M, Michalke B, Schmitt-Kopplin P, Fedorak R, Haller D: Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with IBD. Gut. 2017 May;66(5):863-871. doi: 10.1136/gutjnl-2015-309940. Epub 2016 Feb 4. [PubMed:26848182 ]
Associated OMIM IDsNone
DrugBank IDDB02448
Phenol Explorer Compound IDNot Available
FooDB IDFDB010409
KNApSAcK IDC00007422
Chemspider ID12013
KEGG Compound IDC17076
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkTridecylic acid
METLIN ID5866
PubChem Compound12530
PDB IDNot Available
ChEBI ID45919
Food Biomarker OntologyNot Available
VMH IDM03051
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceKehoe, Lawrence J.; Schell, Raymond A. n-Heptanoic and n-tridecanoic acids from olefins, carbon monoxide and water. Ger. Offen. (1970), 17 pp.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Lee SH, Nam SY, Chung BC: Altered profile of endogenous steroids in the urine of patients with prolactinoma. Clin Biochem. 1998 Oct;31(7):529-35. [PubMed:9812172 ]
  2. Alcorn SM, Orum TV, Steigerwalt AG, Foster JL, Fogleman JC, Brenner DJ: Taxonomy and pathogenicity of Erwinia cacticida sp. nov. Int J Syst Bacteriol. 1991 Apr;41(2):197-212. [PubMed:1854634 ]
  3. Goldschmidt JC Jr, Panos C: Teichoic acids of Streptococcus agalactiae: chemistry, cytotoxicity, and effect on bacterial adherence to human cells in tissue culture. Infect Immun. 1984 Feb;43(2):670-7. [PubMed:6363297 ]

Only showing the first 10 proteins. There are 65 proteins in total.

Enzymes

General function:
Involved in transferase activity
Specific function:
Fatty acid synthetase catalyzes the formation of long-chain fatty acids from acetyl-CoA, malonyl-CoA and NADPH. This multifunctional protein has 7 catalytic activities and an acyl carrier protein.
Gene Name:
FASN
Uniprot ID:
P49327
Molecular weight:
273424.06
General function:
Involved in phospholipase A2 activity
Specific function:
PA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. This isozyme hydrolyzes more efficiently L-alpha-1-palmitoyl-2-oleoyl phosphatidylcholine than L-alpha-1-palmitoyl-2-arachidonyl phosphatidylcholine, L-alpha-1-palmitoyl-2-arachidonyl phosphatidylethanolamine, or L-alpha-1-stearoyl-2-arachidonyl phosphatidylinositol. May be involved in the production of lung surfactant, the remodeling or regulation of cardiac muscle.
Gene Name:
PLA2G5
Uniprot ID:
P39877
Molecular weight:
15674.065
General function:
Involved in phospholipase A2 activity
Specific function:
PA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. Hydrolyzes phosphatidylglycerol versus phosphatidylcholine with a 15-fold preference.
Gene Name:
PLA2G2F
Uniprot ID:
Q9BZM2
Molecular weight:
23256.29
General function:
Involved in metabolic process
Specific function:
Selectively hydrolyzes arachidonyl phospholipids in the sn-2 position releasing arachidonic acid. Together with its lysophospholipid activity, it is implicated in the initiation of the inflammatory response.
Gene Name:
PLA2G4A
Uniprot ID:
P47712
Molecular weight:
85210.19
General function:
Involved in phospholipase A2 activity
Specific function:
PA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.
Gene Name:
PLA2G1B
Uniprot ID:
P04054
Molecular weight:
16359.535
References
  1. 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. [PubMed:10592235 ]
General function:
Involved in phospholipase A2 activity
Specific function:
PA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. Has a powerful potency for releasing arachidonic acid from cell membrane phospholipids. Prefers phosphatidylethanolamine and phosphatidylcholine liposomes to those of phosphatidylserine.
Gene Name:
PLA2G10
Uniprot ID:
O15496
Molecular weight:
18153.04
General function:
Involved in sugar binding
Specific function:
Has lysophospholipase activity.
Gene Name:
LGALS13
Uniprot ID:
Q9UHV8
Molecular weight:
16118.44
General function:
Involved in phospholipase A2 activity
Specific function:
PA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. Has a preference for arachidonic-containing phospholipids.
Gene Name:
PLA2G2E
Uniprot ID:
Q9NZK7
Molecular weight:
15988.525
References
  1. 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. [PubMed:10592235 ]
General function:
Involved in phospholipase A2 activity
Specific function:
PA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. Does not exhibit detectable activity toward sn-2-arachidonoyl- or linoleoyl-phosphatidylcholine or -phosphatidylethanolamine.
Gene Name:
PLA2G12A
Uniprot ID:
Q9BZM1
Molecular weight:
21066.99
General function:
Involved in metabolic process
Specific function:
Catalyzes the release of fatty acids from phospholipids. It has been implicated in normal phospholipid remodeling, nitric oxide-induced or vasopressin-induced arachidonic acid release and in leukotriene and prostaglandin production. May participate in fas mediated apoptosis and in regulating transmembrane ion flux in glucose-stimulated B-cells. Has a role in cardiolipin (CL) deacylation. Required for both speed and directionality of monocyte MCP1/CCL2-induced chemotaxis through regulation of F-actin polymerization at the pseudopods. Isoform ankyrin-iPLA2-1 and isoform ankyrin-iPLA2-2, which lack the catalytic domain, are probably involved in the negative regulation of iPLA2 activity.
Gene Name:
PLA2G6
Uniprot ID:
O60733
Molecular weight:
84092.635

Transporters

General function:
Lipid transport and metabolism
Specific function:
Involved in translocation of long-chain fatty acids (LFCA) across the plasma membrane. The LFCA import appears to be hormone-regulated in a tissue-specific manner. In adipocytes, but not myocytes, insulin induces a rapid translocation of FATP1 from intracellular compartments to the plasma membrane, paralleled by increased LFCA uptake. May act directly as a bona fide transporter, or alternatively, in a cytoplasmic or membrane- associated multimeric protein complex to trap and draw fatty acids towards accumulation. Plays a pivotal role in regulating available LFCA substrates from exogenous sources in tissues undergoing high levels of beta-oxidation or triglyceride synthesis. May be involved in regulation of cholesterol metabolism. Has acyl-CoA ligase activity for long-chain and very-long-chain fatty acids
Gene Name:
SLC27A1
Uniprot ID:
Q6PCB7
Molecular weight:
71107.5

Only showing the first 10 proteins. There are 65 proteins in total.