Bovine Metabolome Database: Showing metabocard for L-Pipecolic acid (BMDB0000716)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (1) Show 1 protein XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:35:24 UTC

Update Date

2020-05-11 20:21:26 UTC

BMDB ID

BMDB0000716

Secondary Accession Numbers

BMDB00716

Metabolite Identification

Common Name

L-Pipecolic acid

Description

L-Pipecolic acid, also known as (S)-pipecolate or L-homoproline, belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom. L-Pipecolic acid exists as a solid, possibly soluble (in water), and a very strong basic compound (based on its pKa) molecule. L-Pipecolic acid has been linked to several inborn metabolic disorders including peroxisomal biogenesis defect and adrenoleukodystrophy.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(S)-(-)-Pipecolic acid	ChEBI
(S)-Pipecolic acid	ChEBI
(S)-Piperidine-2-carboxylic acid	ChEBI
2-Piperidinecarboxylic acid	ChEBI
L-(-)-Pipecolic acid	ChEBI
Pipecolic acid	ChEBI
Pipecolinic acid	ChEBI
(S)-(-)-Pipecolate	Generator
(S)-Pipecolate	Generator
(S)-Piperidine-2-carboxylate	Generator
2-Piperidinecarboxylate	Generator
L-(-)-Pipecolate	Generator
Pipecolate	Generator
Pipecolinate	Generator
L-Pipecolate	Generator
(-)-Pipecolate	HMDB
(-)-Pipecolic acid	HMDB
(S)-(-)-2-Piperidinecarboxylate	HMDB
(S)-(-)-2-Piperidinecarboxylic acid	HMDB
(S)-2-Piperidinecarboxylate	HMDB
(S)-2-Piperidinecarboxylic acid	HMDB
(S)-Pipecolinate	HMDB
(S)-Pipecolinic acid	HMDB
L-Homoproline	HMDB
L-Pipecolinate	HMDB
L-Pipecolinic acid	HMDB
L-Piperidine-2-carboxylate	HMDB
L-Piperidine-2-carboxylic acid	HMDB
Pipecolic acid, (+,-)-isomer	HMDB
Pipecolic acid, 14C-labeled CPD, (+,-)-isomer	HMDB
Homopipecolic acid	HMDB
Pipecolic acid, ion(1-), (+,-)-isomer	HMDB
Pipecolic acid, ion(1-), (S)-isomer	HMDB
Pipecolic acid hydrochloride, (+-)-isomer	HMDB
Pipecolic acid, (S)-isomer	HMDB
Pipecolic acid, (R)-isomer	HMDB
Pipecolic acid, ion (1-)	HMDB
Pipecolic acid, monopotassium salt	HMDB
(2S)-2-Piperidinecarboxylic acid	HMDB
(-)-Pipecolinic acid	HMDB
(2S)-Piperidine-2-carboxylic acid	HMDB
(RS)-2-Piperidinecarboxylic acid	HMDB
(±)-2-piperidinecarboxylic acid	HMDB
(±)-pipecolic acid	HMDB
(±)-pipecolinic acid	HMDB
2-Carboxypiperidine	HMDB
2-Pipecolinic acid	HMDB
2-Piperidinylcarboxylic acid	HMDB
DL-2-Piperidinecarboxylic acid	HMDB
DL-Pipecolic acid	HMDB
DL-Pipecolinic acid	HMDB
Dihydrobaikiane	HMDB
Hexahydro-2-picolinic acid	HMDB
Homoproline	HMDB
Piperidine-6-carboxylic acid	HMDB
Piperolinic acid	HMDB
alpha-Pipecolinic acid	HMDB
Α-pipecolinic acid	HMDB
L-Pipecolic acid	PhytoBank

Chemical Formula

C₆H₁₁NO₂

Average Molecular Weight

129.157

Monoisotopic Molecular Weight

129.078978601

IUPAC Name

(2S)-piperidine-2-carboxylic acid

Traditional Name

L-pipecolic acid

CAS Registry Number

3105-95-1

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-/m0/s1

InChI Key

HXEACLLIILLPRG-YFKPBYRVSA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-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

L-alpha-amino acids

Alternative Parents

Substituents

L-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:30913 )
Piperidine alkaloids (C00408 )

Ontology

Status

Detected but not Quantified

Origin

Endogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Peroxisome

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	272 °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	13.49 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-0a4i-0900000000-c7875e682dfb275cdf1e	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (1 TMS)	splash10-001i-9100000000-07741b1b7d650447197e	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (2 TMS)	splash10-0a4i-1900000000-1b1313072749567d8a9e	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (1 MEOX; 2 TMS)	splash10-0pb9-3960000000-8e89c177d71b5faabdb2	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0a4i-0900000000-c7875e682dfb275cdf1e	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0a4i-1900000000-1b1313072749567d8a9e	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0pb9-3960000000-8e89c177d71b5faabdb2	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-001i-9100000000-07741b1b7d650447197e	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-001i-9100000000-335cf7f41fca5cbc84cf	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-05fu-9700000000-8003521353d4d37af49f	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, N/A (Annotated)	splash10-001i-8900000000-b67eb6eabd8fb1b2824a	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, N/A (Annotated)	splash10-001i-9000000000-b01a5574139ce1222c4d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, N/A (Annotated)	splash10-0a4i-9000000000-d80733b289711920626b	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-004i-0900000000-6d82525e15d98dd794db	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-004i-0900000000-abb8b4f2daaa91bfa758	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-004i-1900000000-b668d1df137fa1685b6d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative	splash10-0002-9000000000-5ec763c9c55715bd01df	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative	splash10-0002-9000000000-5a62167bd787768808f7	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-001i-0900000000-edd41fa2c224ec5f5a1e	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-001i-9100000000-7ed3d7197cd0f23403b6	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-001i-9000000000-e5b2220b7410a3429b95	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-001i-9000000000-baf8dab4263881ac49ea	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive	splash10-0a59-9000000000-d1dc7829582bfd61d47b	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-004i-0900000000-6d82525e15d98dd794db	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-004i-0900000000-abb8b4f2daaa91bfa758	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-004i-1900000000-b668d1df137fa1685b6d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0002-9000000000-5ec763c9c55715bd01df	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0002-9000000000-5a62167bd787768808f7	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-001i-0900000000-edd41fa2c224ec5f5a1e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-3900000000-bf71d20a7c8e71d335e5	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001i-9400000000-fa70645b026293d659de	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-053u-9000000000-f849cc3c4b11bc7d4de7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-2900000000-bf800b5cd197887a11d5	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-003r-7900000000-8a0e9f51df4006740863	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-001i-9000000000-effc196b5c15971f985a	View in MoNA
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Peroxisome

Biospecimen Locations

Liver
Milk

Pathways

Name	SMPDB/Pathwhiz	KEGG
Lysine Degradation		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Liver	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Milk	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 28306241	details
Milk	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 29291809	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0000716

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

30913

References

Synthesis Reference

Kisfaludy, Lajos; Korenczki, Ferenc; Katho, Agnes. Works, Gedeon Richter Ltd., Budapest, Hung. One-step synthesis of L-piperidine-2-carboxylic acid. Synthesis (1982), (2), 163.

Material Safety Data Sheet (MSDS)

Not Available

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 ]
Mung D, Li L: Applying quantitative metabolomics based on chemical isotope labeling LC-MS for detecting potential milk adulterant in human milk. Anal Chim Acta. 2018 Feb 25;1001:78-85. doi: 10.1016/j.aca.2017.11.019. Epub 2017 Nov 14. [PubMed:29291809 ]

Enzymes

Enzyme Details

1. Peroxisomal sarcosine oxidase

General function:: Amino acid transport and metabolism
Specific function:: Metabolizes sarcosine, L-pipecolic acid and L-proline.
Gene Name:: PIPOX
Uniprot ID:: Q29RU9
Molecular weight:: 43820.0

Showing metabocard for L-Pipecolic acid (BMDB0000716)

Structure for BMDB0000716 (L-Pipecolic acid)

Enzymes