Showing metabocard for D-Pipecolic acid (BMDB0005960)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-09-30 23:19:23 UTC
Update Date2020-04-22 15:16:35 UTC
BMDB IDBMDB0005960
Secondary Accession Numbers
  • BMDB05960
Metabolite Identification
Common NameD-Pipecolic acid
DescriptionD-Pipecolic acid, also known as 6-carboxypiperidine or (R)-pipecolate, belongs to the class of organic compounds known as d-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom. D-Pipecolic acid exists as a solid, possibly soluble (in water), and a very strong basic compound (based on its pKa) molecule.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
(R)-Pipecolic acidChEBI
(R)-Piperidine-2-carboxylic acidChEBI
6-CARBOXYPIPERIDINEChEBI
(R)-PipecolateGenerator
(R)-Piperidine-2-carboxylateGenerator
D-PipecolateGenerator
(+)-Pipecolic acidHMDB
(+)-Pipecolinic acidHMDB
(2R)-2-Piperidinecarboxylic acidHMDB
(2R)-Piperidine-2-carboxylic acidHMDB
(R)-()-2-Piperidinecarboxylic acidHMDB
(R)-(+)-Pipecolic acidHMDB
(R)-2-Piperidinecarboxylic acidHMDB
(R)-Pipecolinic acidHMDB
D-(+)- Pipecolic acidHMDB
D-(+)-Pipecolic acidHMDB
D-HomoprolineHMDB
D-Pipecolinic acidHMDB
D-Piperidine-2-carboxylic acidHMDB
Chemical FormulaC6H11NO2
Average Molecular Weight129.157
Monoisotopic Molecular Weight129.078978601
IUPAC Name(2R)-piperidine-2-carboxylic acid
Traditional Name(+)-pipecolic acid
CAS Registry Number1723-00-8
SMILES
OC(=O)[C@H]1CCCCN1
InChI Identifier
InChI=1S/C6H11NO2/c8-6(9)5-3-1-2-4-7-5/h5,7H,1-4H2,(H,8,9)/t5-/m1/s1
InChI KeyHXEACLLIILLPRG-RXMQYKEDSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as d-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentD-alpha-amino acids
Alternative Parents
Substituents
  • D-alpha-amino acid
  • Piperidinecarboxylic acid
  • Piperidine
  • Amino acid
  • Carboxylic acid
  • Secondary aliphatic amine
  • Monocarboxylic acid or derivatives
  • Secondary amine
  • Organoheterocyclic compound
  • Azacycle
  • Organic oxygen compound
  • Organic nitrogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Carbonyl group
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
StatusDetected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locationsNot Available
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point266 - 268 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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 FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Milk
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
MilkDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
Abnormal Concentrations
Not Available
HMDB IDHMDB0005960
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023791
KNApSAcK IDNot Available
Chemspider ID643442
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPipecolic acid
METLIN IDNot Available
PubChem Compound736316
PDB IDNot Available
ChEBI ID41582
References
Synthesis ReferenceFadel, Antoine; Lahrache, Nabil. An efficient synthesis of enantiomerically pure (R)-pipecolic acid, (S)-proline, and their N-alkylated derivatives. Journal of Organic Chemistry (2007), 72(5), 1780-1784.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Mung D, Li L: Development of Chemical Isotope Labeling LC-MS for Milk Metabolomics: Comprehensive and Quantitative Profiling of the Amine/Phenol Submetabolome. Anal Chem. 2017 Apr 18;89(8):4435-4443. doi: 10.1021/acs.analchem.6b03737. Epub 2017 Mar 28. [PubMed:28306241 ]