Showing Compound Pipecolic acid (FDB000545)

Record Information

Version

1.0

Creation date

2010-04-08 22:04:36 UTC

Update date

2019-11-26 02:54:57 UTC

Primary ID

FDB000545

Secondary Accession Numbers

Not Available

Chemical Information

FooDB Name

Pipecolic acid

Description

Pipecolic 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 Number

535-75-1

Structure

MOL SDF PDB SMILES InChI

Synonyms

Synonym	Source
2-Piperidinecarboxylic acid	ChEBI
Homoproline	ChEBI
Pipecolinic acid	ChEBI
2-Piperidinecarboxylate	Generator
Pipecolinate	Generator
Pipecolate	Generator
()-Piperidine-2-carboxylic acid	HMDB
(+/-)-2-piperidinecarboxylate	HMDB
(+/-)-2-piperidinecarboxylic acid	HMDB
(+/-)-pipecolate	HMDB
(+/-)-pipecolic acid	HMDB
(+/-)-pipecolinate	HMDB
(+/-)-pipecolinic acid	HMDB
(.+/-.)-2-piperidinecarboxylic acid	HMDB
(RS)-2-Piperidinecarboxylate	HMDB
(RS)-2-Piperidinecarboxylic acid	HMDB
.alpha.-pipecolinic acid	HMDB
2-Carboxypiperidine	HMDB
2-Pipecolinic acid	HMDB
2-Piperidinylcarboxylic acid	HMDB
a-Pipecolinate	HMDB
a-Pipecolinic acid	HMDB
Acide pipecolique	HMDB
Acide piperidine-carboxylique-2	HMDB
alpha-Pipecolinate	HMDB
alpha-Pipecolinic acid	HMDB
Dihydrobaikiane	HMDB
DL-2-Piperidinecarboxylate	HMDB
DL-2-Piperidinecarboxylic acid	HMDB
DL-Homoproline	HMDB
DL-Pipecolate	HMDB, Generator
DL-Pipecolic acid	HMDB
DL-Pipecolinate	HMDB
DL-Pipecolinic acid	HMDB
hexahydro-2-Picolinate	HMDB
hexahydro-2-Picolinic acid	HMDB
Hexahydropicolinate	HMDB
Hexahydropicolinic acid	HMDB
Pipecolic acid free base	HMDB
Piperidine-2-carboxylic acid	HMDB
Piperolinate	HMDB
Piperolinic acid	HMDB
L-Pipecolic acid	MeSH, HMDB
Pipecolic acid, (R)-isomer	MeSH, HMDB
Pipecolic acid, ion (1-)	MeSH, HMDB
Pipecolic acid, monopotassium salt	MeSH, HMDB
Pipecolic acid hydrochloride, (+-)-isomer	MeSH, HMDB
Pipecolic acid, (S)-isomer	MeSH, HMDB
Pipecolic acid, 14C-labeled CPD, (+,-)-isomer	MeSH, HMDB
Homopipecolic acid	MeSH, HMDB
Pipecolic acid, (+,-)-isomer	MeSH, HMDB
Pipecolic acid, ion(1-), (+,-)-isomer	MeSH, HMDB
Pipecolic acid, ion(1-), (S)-isomer	MeSH, HMDB
Piperidine-2-carboxylate	Generator, HMDB
Pipecolic acid	MeSH
(RS)-2-piperidinecarboxylate	HMDB
(RS)-2-piperidinecarboxylic acid	HMDB
Homoproline?	db_source

Predicted Properties

Property	Value	Source
Water Solubility	158 g/L	ALOGPS
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	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Chemical Formula

C6H11NO2

IUPAC name

piperidine-2-carboxylic acid

InChI Identifier

InChI=1S/C6H11NO2/c8-6(9)5-3-1-2-4-7-5/h5,7H,1-4H2,(H,8,9)

InChI Key

HXEACLLIILLPRG-UHFFFAOYSA-N

Isomeric SMILES

OC(=O)C1CCCCN1

Average Molecular Weight

129.157

Monoisotopic Molecular Weight

129.078978601

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).

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha 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 Framework

Aliphatic heteromonocyclic compounds

External Descriptors

piperidinemonocarboxylic acid (CHEBI:17964 )

Ontology

Physiological effect

Health effect:

Observation:

Periodontal Probing Depth

Health condition:

Blood and lymphatic system disorders:

Anemia

Disposition

Route of exposure:

Enteral:

Ingestion

Source:

Biological:

Microbe

Plant:

Biological location:

Organ and components:

Biofluid and excreta:

Subcellular:

Cytoplasm

Cell and elements:

Extracellular

Physico-Chemical Properties - Experimental

Property	Value	Reference
Physical state	Solid
Physical Description	Not Available
Mass Composition	C 55.80%; H 8.58%; N 10.84%; O 24.77%	DFC
Melting Point	Not Available
Boiling Point	Not Available
Experimental Water Solubility	Not Available
Experimental logP	Not Available
Experimental pKa	Not Available
Isoelectric point	Not Available
Charge	Not Available
Optical Rotation	Not Available
Spectroscopic UV Data	Not Available
Density	Not Available
Refractive Index	Not Available

Spectra

EI-MS/GC-MS

Type	Description	Splash Key	View
GC-MS	Pipecolic acid, non-derivatized, GC-MS Spectrum	splash10-0a4i-0910000000-d9cfd443adb5187a3f21	Spectrum
GC-MS	Pipecolic acid, non-derivatized, GC-MS Spectrum	splash10-0a4i-0910000000-d9cfd443adb5187a3f21	Spectrum
GC-MS	Pipecolic acid, non-derivatized, GC-MS Spectrum	splash10-0a4i-0910000000-d9cfd443adb5187a3f21	Spectrum
GC-MS	Pipecolic acid, non-derivatized, GC-MS Spectrum	splash10-0a4i-0910000000-d9cfd443adb5187a3f21	Spectrum
Predicted GC-MS	Pipecolic acid, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-001i-9200000000-5c4f6059bcc868ca23fd	Spectrum
Predicted GC-MS	Pipecolic acid, 1 TMS, Predicted GC-MS Spectrum - 70eV, Positive	splash10-05fu-9700000000-8003521353d4d37af49f	Spectrum
Predicted GC-MS	Pipecolic acid, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pipecolic acid, TMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pipecolic acid, TBDMS_1_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Pipecolic acid, TBDMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum

MS/MS

Type	Description	Splash Key	View
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0060-9900000000-c5b5bf28424d5d5d1bda	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-001i-9000000000-92660ad26bff36fba7ef	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0a59-9000000000-b779372fa816467754c1	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-001i-9300000000-26dee47121401990f1c1	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) 30V, Positive	splash10-001i-9000000000-929057dfd61546bee24d	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-004i-0900000000-6595801dc6a322f712f0	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-004i-0900000000-6595801dc6a322f712f0	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - , negative	splash10-004i-0900000000-99a7a942cee58c76115a	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-001i-9300000000-26dee47121401990f1c1	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-001i-9000000000-929057dfd61546bee24d	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - , positive	splash10-001i-9600000000-9631d0fbc984509f8d1e	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - 30V, Positive	splash10-001i-9000000000-b244255a58ffb3b92be5	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 35V, Positive	splash10-001i-9000000000-c3041e7b5b1f5118c1ec	2021-09-20	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-3900000000-b2ceb4c88f50a6524604	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001i-9400000000-d3fab76e3fbfbe92c14d	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a5c-9000000000-20464a5c62992da01ab7	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-2900000000-6fac2bf48ffe4d910118	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-003r-8900000000-81b6d69c7a568e36b49f	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-001i-9000000000-6332d1986eb0da0057fd	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-0900000000-b487cd2a72f17977a8cd	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01t9-1900000000-83b59287dc6d3e726326	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0036-9200000000-3ca813e7348e686ed922	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-9300000000-cb8df30f7267d610fd8d	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001i-9000000000-72c8691eb15dce6e0abb	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-053r-9000000000-c7623c5058ad6c879ec3	2021-09-22	View Spectrum

NMR

Type	Description	View
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H 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

External Links

ChemSpider ID

ChEMBL ID

KEGG Compound ID

Pubchem Compound ID

Pubchem Substance ID

Not Available

ChEBI ID

Not Available

Phenol-Explorer ID

Not Available

DrugBank ID

Not Available

HMDB ID

HMDB00070

CRC / DFC (Dictionary of Food Compounds) ID

BDK62-V:BDK62-V

EAFUS ID

Not Available

Dr. Duke ID

PIPECOLINIC-ACID|L-PIPECOLIC-ACID|PIPECOLIC-ACID

BIGG ID

Not Available

KNApSAcK ID

C00001387

HET ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

Flavornet ID

Not Available

GoodScent ID

Not Available

SuperScent ID

Not Available

Wikipedia ID

Not Available

Phenol-Explorer Metabolite ID

Not Available

Duplicate IDS

Not Available

Old DFC IDS

Not Available

Associated Foods

Food	Content Range	Average	Reference
Food			Reference

Biological Effects and Interactions

Health Effects / Bioactivities

Descriptor	ID	Definition	Reference
herbistat			DUKE
pesticide	25944	Strictly, a substance intended to kill pests. In common usage, any substance used for controlling, preventing, or destroying animal, microbiological or plant pests.	DUKE