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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
Not AvailableNot Available
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
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-c5b5bf28424d5d5d1bda2012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-001i-9000000000-92660ad26bff36fba7ef2012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0a59-9000000000-b779372fa816467754c12012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-001i-9300000000-26dee47121401990f1c12012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) 30V, Positivesplash10-001i-9000000000-929057dfd61546bee24d2012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-004i-0900000000-6595801dc6a322f712f02012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-004i-0900000000-6595801dc6a322f712f02017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - , negativesplash10-004i-0900000000-99a7a942cee58c76115a2017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-001i-9300000000-26dee47121401990f1c12017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-001i-9000000000-929057dfd61546bee24d2017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - , positivesplash10-001i-9600000000-9631d0fbc984509f8d1e2017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - 30V, Positivesplash10-001i-9000000000-b244255a58ffb3b92be52021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-001i-9000000000-c3041e7b5b1f5118c1ec2021-09-20View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-3900000000-b2ceb4c88f50a65246042015-05-27View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-9400000000-d3fab76e3fbfbe92c14d2015-05-27View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a5c-9000000000-20464a5c62992da01ab72015-05-27View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-2900000000-6fac2bf48ffe4d9101182015-05-27View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-003r-8900000000-81b6d69c7a568e36b49f2015-05-27View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-001i-9000000000-6332d1986eb0da0057fd2015-05-27View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-0900000000-b487cd2a72f17977a8cd2021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01t9-1900000000-83b59287dc6d3e7263262021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0036-9200000000-3ca813e7348e686ed9222021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-9300000000-cb8df30f7267d610fd8d2021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-9000000000-72c8691eb15dce6e0abb2021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-053r-9000000000-c7623c5058ad6c879ec32021-09-22View Spectrum
NMR
TypeDescriptionView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Spectrum
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Spectrum
2D NMR[1H, 1H]-TOCSY. Unexported temporarily by An Chi on Oct 15, 2021 until json or nmrML file is generated. 2D NMR Spectrum (experimental)Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Spectrum
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.