Milk Composition Database: Showing metabocard for D-Pipecolic acid (BMDB0005960)

Identification Taxonomy Physical properties Spectra Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-09-30 23:19:23 UTC

Update Date

2020-04-22 15:16:35 UTC

MCDB ID

BMDB0005960

Secondary Accession Numbers

BMDB05960

Metabolite Identification

Common Name

D-Pipecolic acid

Description

D-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

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(R)-Pipecolic acid	ChEBI
(R)-Piperidine-2-carboxylic acid	ChEBI
6-CARBOXYPIPERIDINE	ChEBI
(R)-Pipecolate	Generator
(R)-Piperidine-2-carboxylate	Generator
D-Pipecolate	Generator
(+)-Pipecolic acid	HMDB
(+)-Pipecolinic acid	HMDB
(2R)-2-Piperidinecarboxylic acid	HMDB
(2R)-Piperidine-2-carboxylic acid	HMDB
(R)-()-2-Piperidinecarboxylic acid	HMDB
(R)-(+)-Pipecolic acid	HMDB
(R)-2-Piperidinecarboxylic acid	HMDB
(R)-Pipecolinic acid	HMDB
D-(+)- Pipecolic acid	HMDB
D-(+)-Pipecolic acid	HMDB
D-Homoproline	HMDB
D-Pipecolinic acid	HMDB
D-Piperidine-2-carboxylic acid	HMDB

Chemical Formula

C₆H₁₁NO₂

Average Molecular Weight

129.157

Monoisotopic Molecular Weight

129.078978601

IUPAC Name

(2R)-piperidine-2-carboxylic acid

Traditional Name

(+)-pipecolic acid

CAS Registry Number

1723-00-8

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 Key

HXEACLLIILLPRG-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.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

D-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 Framework

Aliphatic heteromonocyclic compounds

External Descriptors

pipecolic acid (CHEBI:41582 )

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	266 - 268 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-2.2	ALOGPS
logP	-2.1	ChemAxon
logS	0.09	ALOGPS
pKa (Strongest Acidic)	2.06	ChemAxon
pKa (Strongest Basic)	10.39	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	49.33 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	32.67 m³·mol⁻¹	ChemAxon
Polarizability	13.47 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-001i-9100000000-335cf7f41fca5cbc84cf	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-001i-9100000000-4611bf819d3b9d4fd062	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-3900000000-bf71d20a7c8e71d335e5	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001i-9400000000-fa70645b026293d659de	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-053u-9000000000-f849cc3c4b11bc7d4de7	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-2900000000-bf800b5cd197887a11d5	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-003r-7900000000-8a0e9f51df4006740863	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-001i-9000000000-effc196b5c15971f985a	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-9300000000-cb8df30f7267d610fd8d	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001i-9000000000-72c8691eb15dce6e0abb	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-053r-9000000000-c7623c5058ad6c879ec3	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-0900000000-b487cd2a72f17977a8cd	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01t9-1900000000-83b59287dc6d3e726326	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0036-9200000000-3ca813e7348e686ed922	2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	2021-09-24	View Spectrum

Concentrations

Status	Value		Reference	Details
Detected but not Quantified	Not Applicable		PMID: 28306241	details

External Links

HMDB ID

HMDB0005960

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB023791

KNApSAcK ID

Not Available

Chemspider ID

643442

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Pipecolic acid

METLIN ID

Not Available

PubChem Compound

736316

PDB ID

Not Available

ChEBI ID

41582

References

Synthesis Reference

Fadel, 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)

Download (PDF)

General References

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 ]

Showing metabocard for D-Pipecolic acid (BMDB0005960)

Structure for BMDB0005960 (D-Pipecolic acid)