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Showing Compound Pipecolic acid (FDB000545)

Record Information
Version1.0
Creation date2010-04-08 22:04:36 UTC
Update date2019-11-26 02:54:57 UTC
Primary IDFDB000545
Secondary Accession NumbersNot Available
Chemical Information
FooDB NamePipecolic acid
DescriptionPipecolic acid is a metabolite of lysine found in human physiological fluids such as urine, plasma and CSF. However, it is uncertain if pipecolic acid originates directly from food intake or from mammalian or intestinal bacterial enzyme metabolism. Recent studies suggest that plasma pipecolic acid, particularly the D-isomer, originates mainly from the catabolism of dietary lysine by intestinal bacteria rather than by direct food intake. In classic Zellweger syndrome (a cerebro-hepato-renal genetic disorder, OMIM 214100) pipecolic acid accumulate in the plasma of the patients. It is known that plasma pipecolic acid levels are also elevated in patients with chronic liver diseases. Pipecolic acid is moderately elevated in patients with pyridoxine-dependent seizures and might therefore be a possible biochemical marker for selecting candidates for pyridoxine therapy (Plecko et al 2000). Pipecolic acid was also elevated in CSF in these vitamin B6-responsive patients. (PMID 12705501) [HMDB]. Pipecolic acid is a biomarker for the consumption of dried and cooked beans.
CAS Number535-75-1
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
SynonymSource
2-Piperidinecarboxylic acidChEBI
HomoprolineChEBI
Pipecolinic acidChEBI
2-PiperidinecarboxylateGenerator
PipecolinateGenerator
PipecolateGenerator
()-Piperidine-2-carboxylic acidHMDB
(+/-)-2-piperidinecarboxylateHMDB
(+/-)-2-piperidinecarboxylic acidHMDB
(+/-)-pipecolateHMDB
(+/-)-pipecolic acidHMDB
(+/-)-pipecolinateHMDB
(+/-)-pipecolinic acidHMDB
(.+/-.)-2-piperidinecarboxylic acidHMDB
(RS)-2-PiperidinecarboxylateHMDB
(RS)-2-Piperidinecarboxylic acidHMDB
.alpha.-pipecolinic acidHMDB
2-CarboxypiperidineHMDB
2-Pipecolinic acidHMDB
2-Piperidinylcarboxylic acidHMDB
a-PipecolinateHMDB
a-Pipecolinic acidHMDB
Acide pipecoliqueHMDB
Acide piperidine-carboxylique-2HMDB
alpha-PipecolinateHMDB
alpha-Pipecolinic acidHMDB
DihydrobaikianeHMDB
DL-2-PiperidinecarboxylateHMDB
DL-2-Piperidinecarboxylic acidHMDB
DL-HomoprolineHMDB
DL-PipecolateHMDB, Generator
DL-Pipecolic acidHMDB
DL-PipecolinateHMDB
DL-Pipecolinic acidHMDB
hexahydro-2-PicolinateHMDB
hexahydro-2-Picolinic acidHMDB
HexahydropicolinateHMDB
Hexahydropicolinic acidHMDB
Pipecolic acid free baseHMDB
Piperidine-2-carboxylic acidHMDB
PiperolinateHMDB
Piperolinic acidHMDB
L-Pipecolic acidMeSH, HMDB
Pipecolic acid, (R)-isomerMeSH, HMDB
Pipecolic acid, ion (1-)MeSH, HMDB
Pipecolic acid, monopotassium saltMeSH, HMDB
Pipecolic acid hydrochloride, (+-)-isomerMeSH, HMDB
Pipecolic acid, (S)-isomerMeSH, HMDB
Pipecolic acid, 14C-labeled CPD, (+,-)-isomerMeSH, HMDB
Homopipecolic acidMeSH, HMDB
Pipecolic acid, (+,-)-isomerMeSH, HMDB
Pipecolic acid, ion(1-), (+,-)-isomerMeSH, HMDB
Pipecolic acid, ion(1-), (S)-isomerMeSH, HMDB
Piperidine-2-carboxylateGenerator, HMDB
Pipecolic acidMeSH
(RS)-2-piperidinecarboxylateHMDB
(RS)-2-piperidinecarboxylic acidHMDB
Homoproline?db_source
Predicted Properties
PropertyValueSource
Water Solubility158 g/LALOGPS
logP-2.2ALOGPS
logP-2.1ChemAxon
logS0.09ALOGPS
pKa (Strongest Acidic)2.06ChemAxon
pKa (Strongest Basic)10.39ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area49.33 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity32.67 m³·mol⁻¹ChemAxon
Polarizability13.47 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Chemical FormulaC6H11NO2
IUPAC namepiperidine-2-carboxylic acid
InChI IdentifierInChI=1S/C6H11NO2/c8-6(9)5-3-1-2-4-7-5/h5,7H,1-4H2,(H,8,9)
InChI KeyHXEACLLIILLPRG-UHFFFAOYSA-N
Isomeric SMILESOC(=O)C1CCCCN1
Average Molecular Weight129.157
Monoisotopic Molecular Weight129.078978601
Classification
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
  • Piperidinecarboxylic acid
  • Piperidine
  • Amino acid
  • Azacycle
  • Organoheterocyclic compound
  • Secondary amine
  • Monocarboxylic acid or derivatives
  • Secondary aliphatic amine
  • Carboxylic acid
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Amine
  • Organic nitrogen compound
  • Organic oxide
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effect

Health effect:

Disposition

Route of exposure:

Source:

Biological location:

Physico-Chemical Properties - Experimental
Physico-Chemical Properties - Experimental
PropertyValueReference
Physical stateSolid
Physical DescriptionNot Available
Mass CompositionC 55.80%; H 8.58%; N 10.84%; O 24.77%DFC
Melting PointNot Available
Boiling PointNot Available
Experimental Water SolubilityNot Available
Experimental logPNot Available
Experimental pKaNot Available
Isoelectric pointNot Available
ChargeNot Available
Optical RotationNot Available
Spectroscopic UV DataNot Available
DensityNot Available
Refractive IndexNot Available
Spectra
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
GC-MSPipecolic acid, non-derivatized, GC-MS Spectrumsplash10-0a4i-0910000000-d9cfd443adb5187a3f21Spectrum
GC-MSPipecolic acid, non-derivatized, GC-MS Spectrumsplash10-0a4i-0910000000-d9cfd443adb5187a3f21Spectrum
GC-MSPipecolic acid, non-derivatized, GC-MS Spectrumsplash10-0a4i-0910000000-d9cfd443adb5187a3f21Spectrum
GC-MSPipecolic acid, non-derivatized, GC-MS Spectrumsplash10-0a4i-0910000000-d9cfd443adb5187a3f21Spectrum
Predicted GC-MSPipecolic acid, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-001i-9200000000-5c4f6059bcc868ca23fdSpectrum
Predicted GC-MSPipecolic acid, 1 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-05fu-9700000000-8003521353d4d37af49fSpectrum
Predicted GC-MSPipecolic acid, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPipecolic acid, TMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPipecolic acid, TBDMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPipecolic acid, TBDMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-0060-9900000000-c5b5bf28424d5d5d1bdaSpectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-001i-9000000000-92660ad26bff36fba7efSpectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0a59-9000000000-b779372fa816467754c1Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-001i-9300000000-26dee47121401990f1c1Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) 30V, Positivesplash10-001i-9000000000-929057dfd61546bee24dSpectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-004i-0900000000-6595801dc6a322f712f0Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-004i-0900000000-6595801dc6a322f712f0Spectrum
MS/MSLC-MS/MS Spectrum - , negativesplash10-004i-0900000000-99a7a942cee58c76115aSpectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-001i-9300000000-26dee47121401990f1c1Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-001i-9000000000-929057dfd61546bee24dSpectrum
MS/MSLC-MS/MS Spectrum - , positivesplash10-001i-9600000000-9631d0fbc984509f8d1eSpectrum
MS/MSLC-MS/MS Spectrum - 30V, Positivesplash10-001i-9000000000-b244255a58ffb3b92be5Spectrum
MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-001i-9000000000-c3041e7b5b1f5118c1ecSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-3900000000-b2ceb4c88f50a6524604Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-9400000000-d3fab76e3fbfbe92c14dSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a5c-9000000000-20464a5c62992da01ab7Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-2900000000-6fac2bf48ffe4d910118Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-003r-8900000000-81b6d69c7a568e36b49fSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-001i-9000000000-6332d1986eb0da0057fdSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-0900000000-b487cd2a72f17977a8cdSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01t9-1900000000-83b59287dc6d3e726326Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0036-9200000000-3ca813e7348e686ed922Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-9300000000-cb8df30f7267d610fd8dSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-9000000000-72c8691eb15dce6e0abbSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-053r-9000000000-c7623c5058ad6c879ec3Spectrum
NMR
TypeDescriptionView
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
2D NMR[1H,1H] 2D NMR SpectrumSpectrum
2D NMR[1H,13C] 2D NMR SpectrumSpectrum
ChemSpider ID826
ChEMBL IDCHEMBL308408
KEGG Compound IDC00408
Pubchem Compound ID849
Pubchem Substance IDNot Available
ChEBI IDNot Available
Phenol-Explorer IDNot Available
DrugBank IDNot Available
HMDB IDHMDB00070
CRC / DFC (Dictionary of Food Compounds) IDBDK62-V:BDK62-V
EAFUS IDNot Available
Dr. Duke IDPIPECOLINIC-ACID|L-PIPECOLIC-ACID|PIPECOLIC-ACID
BIGG IDNot Available
KNApSAcK IDC00001387
HET IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
Flavornet IDNot Available
GoodScent IDNot Available
SuperScent IDNot Available
Wikipedia IDNot Available
Phenol-Explorer Metabolite IDNot Available
Duplicate IDSNot Available
Old DFC IDSNot Available
Associated Foods
FoodContent Range AverageReference
FoodReference
Biological Effects and Interactions
Health Effects / Bioactivities
DescriptorIDDefinitionReference
herbistatDUKE
pesticide25944 Strictly, a substance intended to kill pests. In common usage, any substance used for controlling, preventing, or destroying animal, microbiological or plant pests.DUKE
EnzymesNot Available
PathwaysNot Available
MetabolismNot Available
BiosynthesisNot Available
Organoleptic Properties
FlavoursNot Available
Files
MSDSshow
References
Synthesis ReferenceNot Available
General ReferenceNot Available
Content Reference— Duke, James. 'Dr. Duke's Phytochemical and Ethnobotanical Databases. United States Department of Agriculture.' Agricultural Research Service, Accessed April 27 (2004).
— Shinbo, Y., et al. 'KNApSAcK: a comprehensive species-metabolite relationship database.' Plant Metabolomics. Springer Berlin Heidelberg, 2006. 165-181.