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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 15:23:58 UTC
Update Date2021-09-26 23:10:36 UTC
HMDB IDHMDB0255618
Secondary Accession NumbersNone
Metabolite Identification
Common NameNipecotic acid
DescriptionNipecotic acid, also known as nipecotate, belongs to the class of organic compounds known as piperidinecarboxylic acids. Piperidinecarboxylic acids are compounds containing a piperidine ring which bears a carboxylic acid group. Based on a literature review a significant number of articles have been published on Nipecotic acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). Nipecotic acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Nipecotic acid is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
Thumb
Synonyms
ValueSource
3-Piperidinecarboxylic acidChEBI
Hexahydronicotinic acidChEBI
Piperidine-3-carboxylic acidChEBI
3-PiperidinecarboxylateGenerator
HexahydronicotinateGenerator
Piperidine-3-carboxylateGenerator
NipecotateGenerator
(RS)-Nipecotic acidHMDB
Nipecotic acid hydrideHMDB
Nipecotic acid hydrochlorideHMDB
Nipecotic acid, (+-)-isomerHMDB
Nipecotic acid, (R)-isomerHMDB
Nipecotic acid, (S)-isomerHMDB
Chemical FormulaC6H11NO2
Average Molecular Weight129.159
Monoisotopic Molecular Weight129.078978598
IUPAC Namepiperidine-3-carboxylic acid
Traditional Namenipecotic acid
CAS Registry NumberNot Available
SMILES
OC(=O)C1CCCNC1
InChI Identifier
InChI=1S/C6H11NO2/c8-6(9)5-2-1-3-7-4-5/h5,7H,1-4H2,(H,8,9)
InChI KeyXJLSEXAGTJCILF-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as piperidinecarboxylic acids. Piperidinecarboxylic acids are compounds containing a piperidine ring which bears a carboxylic acid group.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPiperidines
Sub ClassPiperidinecarboxylic acids and derivatives
Direct ParentPiperidinecarboxylic acids
Alternative Parents
Substituents
  • Piperidinecarboxylic acid
  • Amino acid or derivatives
  • Amino acid
  • Carboxylic acid derivative
  • Carboxylic acid
  • Secondary aliphatic amine
  • Monocarboxylic acid or derivatives
  • Azacycle
  • Secondary amine
  • Amine
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Carbonyl group
  • Organic nitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
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
logP-2.4ALOGPS
logP-2.4ChemAxon
logS0.16ALOGPS
pKa (Strongest Acidic)3.79ChemAxon
pKa (Strongest Basic)10.24ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area49.33 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity32.92 m³·mol⁻¹ChemAxon
Polarizability13.48 ųChemAxon
Number of Rings1ChemAxon
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]+126.78430932474
DeepCCS[M-H]-124.0530932474
DeepCCS[M-2H]-160.41230932474
DeepCCS[M+Na]+135.61830932474
AllCCS[M+H]+127.432859911
AllCCS[M+H-H2O]+122.732859911
AllCCS[M+NH4]+131.832859911
AllCCS[M+Na]+133.132859911
AllCCS[M-H]-126.632859911
AllCCS[M+Na-2H]-128.832859911
AllCCS[M+HCOO]-131.232859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20228.283 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20225.57 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid430.7 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid277.1 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid60.0 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid177.3 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid61.0 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid265.0 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid230.1 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)760.4 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid546.4 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid39.2 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid626.7 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid182.2 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid200.5 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate828.2 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA474.9 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water290.1 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Nipecotic acidOC(=O)C1CCCNC12071.9Standard polar33892256
Nipecotic acidOC(=O)C1CCCNC11184.2Standard non polar33892256
Nipecotic acidOC(=O)C1CCCNC11270.8Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Nipecotic acid,2TMS,isomer #1C[Si](C)(C)OC(=O)C1CCCN([Si](C)(C)C)C11382.3Semi standard non polar33892256
Nipecotic acid,2TMS,isomer #1C[Si](C)(C)OC(=O)C1CCCN([Si](C)(C)C)C11402.7Standard non polar33892256
Nipecotic acid,2TMS,isomer #1C[Si](C)(C)OC(=O)C1CCCN([Si](C)(C)C)C11683.0Standard polar33892256
Nipecotic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C1CCCN([Si](C)(C)C(C)(C)C)C11878.0Semi standard non polar33892256
Nipecotic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C1CCCN([Si](C)(C)C(C)(C)C)C11838.1Standard non polar33892256
Nipecotic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C1CCCN([Si](C)(C)C(C)(C)C)C11957.6Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Nipecotic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-0a5c-9200000000-d1c4370e5df665c924392021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Nipecotic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Nipecotic acid GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Nipecotic acid GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Nipecotic acid GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Nipecotic acid GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID4342
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNipecotic acid
METLIN IDNot Available
PubChem Compound4498
PDB IDNot Available
ChEBI ID116931
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 References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]