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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:30:21 UTC

Update Date

2022-03-07 02:52:09 UTC

HMDB ID

HMDB0029426

Secondary Accession Numbers

HMDB29426

Metabolite Identification

Common Name

L-trans-5-Hydroxy-2-piperidinecarboxylic acid

Description

L-trans-5-Hydroxy-2-piperidinecarboxylic acid, also known as 5-hydroxypipecolate, 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). L-trans-5-Hydroxy-2-piperidinecarboxylic acid is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on L-trans-5-Hydroxy-2-piperidinecarboxylic acid.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
L-trans-5-Hydroxy-2-piperidinecarboxylate	Generator
L-trans-5-Hydroxypipecolic acid	HMDB
5-Hydroxypipecolic acid, cis-isomer	HMDB
5-Hydroxypipecolic acid, ion (1-)-cis-isomer	HMDB
5-Hydroxypipecolic acid, trans-isomer	HMDB
5-Hydroxypipecolate	HMDB
5-Hydroxypipecolic acid	HMDB

Chemical Formula

C₆H₁₁NO₃

Average Molecular Weight

145.1564

Monoisotopic Molecular Weight

145.073893223

IUPAC Name

5-hydroxypiperidine-2-carboxylic acid

Traditional Name

5-hydroxypiperidine-2-carboxylic acid

CAS Registry Number

50439-45-7

SMILES

OC1CCC(NC1)C(O)=O

InChI Identifier

InChI=1S/C6H11NO3/c8-4-1-2-5(6(9)10)7-3-4/h4-5,7-8H,1-3H2,(H,9,10)

InChI Key

RKEYKDXXZCICFZ-UHFFFAOYSA-N

Chemical Taxonomy

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
1,2-aminoalcohol
Amino acid
Secondary alcohol
Carboxylic acid
Secondary aliphatic amine
Monocarboxylic acid or derivatives
Secondary amine
Organoheterocyclic compound
Azacycle
Organooxygen compound
Organonitrogen compound
Alcohol
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organic oxygen compound
Amine
Carbonyl group
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

piperidinemonocarboxylic acid (CHEBI:74048 )

Ontology

Not Available

Exogenous (HMDB: HMDB29426)

Food

Fruit

Fruits (FooDB: FOOD00871)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	235 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	258 g/L	ALOGPS
logP	-3	ALOGPS
logP	-3.2	ChemAxon
logS	0.25	ALOGPS
pKa (Strongest Acidic)	1.78	ChemAxon
pKa (Strongest Basic)	9.79	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	69.56 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	34.03 m³·mol⁻¹	ChemAxon
Polarizability	14.38 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	131.741	31661259
DarkChem	[M-H]-	128.322	31661259
DeepCCS	[M+H]+	128.345	30932474
DeepCCS	[M-H]-	125.567	30932474
DeepCCS	[M-2H]-	162.069	30932474
DeepCCS	[M+Na]+	136.907	30932474
AllCCS	[M+H]+	132.1	32859911
AllCCS	[M+H-H2O]+	127.5	32859911
AllCCS	[M+NH4]+	136.3	32859911
AllCCS	[M+Na]+	137.5	32859911
AllCCS	[M-H]-	127.8	32859911
AllCCS	[M+Na-2H]-	129.5	32859911
AllCCS	[M+HCOO]-	131.4	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
L-trans-5-Hydroxy-2-piperidinecarboxylic acid	OC1CCC(NC1)C(O)=O	2560.3	Standard polar	33892256
L-trans-5-Hydroxy-2-piperidinecarboxylic acid	OC1CCC(NC1)C(O)=O	1337.3	Standard non polar	33892256
L-trans-5-Hydroxy-2-piperidinecarboxylic acid	OC1CCC(NC1)C(O)=O	1439.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
L-trans-5-Hydroxy-2-piperidinecarboxylic acid,1TMS,isomer #1	C[Si](C)(C)OC1CCC(C(=O)O)NC1	1544.4	Semi standard non polar	33892256
L-trans-5-Hydroxy-2-piperidinecarboxylic acid,1TMS,isomer #2	C[Si](C)(C)OC(=O)C1CCC(O)CN1	1501.7	Semi standard non polar	33892256
L-trans-5-Hydroxy-2-piperidinecarboxylic acid,1TMS,isomer #3	C[Si](C)(C)N1CC(O)CCC1C(=O)O	1509.8	Semi standard non polar	33892256
L-trans-5-Hydroxy-2-piperidinecarboxylic acid,2TMS,isomer #1	C[Si](C)(C)OC(=O)C1CCC(O[Si](C)(C)C)CN1	1565.4	Semi standard non polar	33892256
L-trans-5-Hydroxy-2-piperidinecarboxylic acid,2TMS,isomer #2	C[Si](C)(C)OC1CCC(C(=O)O)N([Si](C)(C)C)C1	1590.3	Semi standard non polar	33892256
L-trans-5-Hydroxy-2-piperidinecarboxylic acid,2TMS,isomer #3	C[Si](C)(C)OC(=O)C1CCC(O)CN1[Si](C)(C)C	1544.7	Semi standard non polar	33892256
L-trans-5-Hydroxy-2-piperidinecarboxylic acid,3TMS,isomer #1	C[Si](C)(C)OC(=O)C1CCC(O[Si](C)(C)C)CN1[Si](C)(C)C	1608.4	Semi standard non polar	33892256
L-trans-5-Hydroxy-2-piperidinecarboxylic acid,3TMS,isomer #1	C[Si](C)(C)OC(=O)C1CCC(O[Si](C)(C)C)CN1[Si](C)(C)C	1649.9	Standard non polar	33892256
L-trans-5-Hydroxy-2-piperidinecarboxylic acid,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1CCC(C(=O)O)NC1	1799.1	Semi standard non polar	33892256
L-trans-5-Hydroxy-2-piperidinecarboxylic acid,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)C1CCC(O)CN1	1746.8	Semi standard non polar	33892256
L-trans-5-Hydroxy-2-piperidinecarboxylic acid,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N1CC(O)CCC1C(=O)O	1765.1	Semi standard non polar	33892256
L-trans-5-Hydroxy-2-piperidinecarboxylic acid,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C1CCC(O[Si](C)(C)C(C)(C)C)CN1	2007.9	Semi standard non polar	33892256
L-trans-5-Hydroxy-2-piperidinecarboxylic acid,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1CCC(C(=O)O)N([Si](C)(C)C(C)(C)C)C1	2074.5	Semi standard non polar	33892256
L-trans-5-Hydroxy-2-piperidinecarboxylic acid,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)C1CCC(O)CN1[Si](C)(C)C(C)(C)C	1998.0	Semi standard non polar	33892256
L-trans-5-Hydroxy-2-piperidinecarboxylic acid,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C1CCC(O[Si](C)(C)C(C)(C)C)CN1[Si](C)(C)C(C)(C)C	2279.5	Semi standard non polar	33892256
L-trans-5-Hydroxy-2-piperidinecarboxylic acid,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C1CCC(O[Si](C)(C)C(C)(C)C)CN1[Si](C)(C)C(C)(C)C	2292.9	Standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - L-trans-5-Hydroxy-2-piperidinecarboxylic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-056r-9300000000-dfd5bcb87712ead45e0c	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-trans-5-Hydroxy-2-piperidinecarboxylic acid GC-MS (2 TMS) - 70eV, Positive	splash10-00di-4920000000-c137749c969db4c3f9a7	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-trans-5-Hydroxy-2-piperidinecarboxylic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - L-trans-5-Hydroxy-2-piperidinecarboxylic acid CE-QTOF-MS system (Agilent 7100 CE + 6550 QTOF) 20V, Positive-QTOF	Not Available	2019-09-10	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-trans-5-Hydroxy-2-piperidinecarboxylic acid 10V, Positive-QTOF	splash10-004i-1900000000-cf03f58c0883bdc02758	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-trans-5-Hydroxy-2-piperidinecarboxylic acid 20V, Positive-QTOF	splash10-003r-7900000000-bff42ab0b681fb65d14f	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-trans-5-Hydroxy-2-piperidinecarboxylic acid 40V, Positive-QTOF	splash10-001i-9100000000-ce01ad999976b4baf5c7	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-trans-5-Hydroxy-2-piperidinecarboxylic acid 10V, Negative-QTOF	splash10-0006-1900000000-824c8cca1889293dffb0	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-trans-5-Hydroxy-2-piperidinecarboxylic acid 20V, Negative-QTOF	splash10-0f9x-3900000000-4c68f6c4925bcb884a3b	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-trans-5-Hydroxy-2-piperidinecarboxylic acid 40V, Negative-QTOF	splash10-0006-9100000000-dc8eb306c4c44ba41e9c	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-trans-5-Hydroxy-2-piperidinecarboxylic acid 10V, Negative-QTOF	splash10-0006-0900000000-3d59768dce8a6fe46dfe	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-trans-5-Hydroxy-2-piperidinecarboxylic acid 20V, Negative-QTOF	splash10-000f-9500000000-c386f694e3efac21f2de	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-trans-5-Hydroxy-2-piperidinecarboxylic acid 40V, Negative-QTOF	splash10-0006-9000000000-497d565ca64ed7fa6ff2	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-trans-5-Hydroxy-2-piperidinecarboxylic acid 10V, Positive-QTOF	splash10-0f6t-1900000000-87958192ec7cd3232317	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-trans-5-Hydroxy-2-piperidinecarboxylic acid 20V, Positive-QTOF	splash10-0ue9-9600000000-5ee3846e74d8ecfc5928	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-trans-5-Hydroxy-2-piperidinecarboxylic acid 40V, Positive-QTOF	splash10-053u-9000000000-0e1caa6dd5889d35fe48	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB000527

KNApSAcK ID

Not Available

Chemspider ID

133730

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

151730

PDB ID

Not Available

ChEBI ID

74048

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for L-trans-5-Hydroxy-2-piperidinecarboxylic acid (HMDB0029426)

MOL for HMDB0029426 (L-trans-5-Hydroxy-2-piperidinecarboxylic acid)

3D MOL for HMDB0029426 (L-trans-5-Hydroxy-2-piperidinecarboxylic acid)

3D SDF for HMDB0029426 (L-trans-5-Hydroxy-2-piperidinecarboxylic acid)

3D-SDF for HMDB0029426 (L-trans-5-Hydroxy-2-piperidinecarboxylic acid)

PDB for HMDB0029426 (L-trans-5-Hydroxy-2-piperidinecarboxylic acid)

3D PDB for HMDB0029426 (L-trans-5-Hydroxy-2-piperidinecarboxylic acid)

SMILES for HMDB0029426 (L-trans-5-Hydroxy-2-piperidinecarboxylic acid)

INCHI for HMDB0029426 (L-trans-5-Hydroxy-2-piperidinecarboxylic acid)

Structure for HMDB0029426 (L-trans-5-Hydroxy-2-piperidinecarboxylic acid)

3D Structure for HMDB0029426 (L-trans-5-Hydroxy-2-piperidinecarboxylic acid)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra