Livestock Metabolome Database: Showing metabocard for 5-Aminopentanoic acid (LMDB00429)

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-07-13 19:49:40 UTC

Update Date

2016-09-23 18:45:26 UTC

Lmdb

LMDB00429

Secondary Accession Numbers

None

Metabolite Identification

Common Name

5-Aminopentanoic acid

Description

5-aminovalerate (or 5-aminopentanoic acid) is a lysine degradation product. It can be produced both endogenously or through bacterial catabolism of lysine. 5-aminovalerate is formed via the following multi-step reaction: L-lysine leads to cadverine leads to L-piperideine leads 5-aminovalerate (PMID: 405455 ). In other words it is a metabolite of cadaverine which is formed via the intermediate, 1-piperideine (PMID: 6436440 ). Cadaverine is a foul-smelling diamine compound produced by protein hydrolysis during putrefaction of animal tissue. High levels of 5-aminovalerate in biofluids may indicate bacterial overgrowth or endogenous tissue necrosis. In most cases endogenous 5-aminovalerate is thought to be primarily a microbial metabolite produced by the gut or oral microflora, although it can be produced endogenously. 5-aminovalerate is a normal metabolite present in animal saliva, with a tendency to elevated concentration in patients with chronic periodontitis. Bacterial contamination and decomposition of salivary proteins is primarily responsible for elevated salivary levels (PMID 3481959 ). Beyond being a general waste product, 5-aminovalerate is also believed to act as a methylene homologue of gamma-aminobutyric acid (GABA) and functions as a weak GABA agonist (PMID: 4031870 ). It is also known as an antifibrinolytic amino acid analog and so it functions as a weak inhibitor of the blood clotting pathway (PMID: 6703712 ). 5-aminopentanoic acid is an in vivo substrate of 4-aminobutyrate:2-oxoglutarate aminotransferase (PMID: 4031870 ).

Structure

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms

Value	Source
5-Amino-N-valeric acid	ChEBI
5-Aminopentanoate	ChEBI
5-Aminovaleric acid	ChEBI
DANVA	ChEBI
delta-Amino-N-valeric acid	ChEBI
delta-Aminovaleric acid	ChEBI
5-Amino-N-valerate	Generator
5-Aminovalerate	Generator
delta-Amino-N-valerate	Generator
Δ-amino-N-valerate	Generator
Δ-amino-N-valeric acid	Generator
delta-Aminovalerate	Generator
Δ-aminovalerate	Generator
Δ-aminovaleric acid	Generator
5-Aminovaleric acid hydrochloride	MeSH
5-Aminopentanoic acid	KEGG
5-Amino-pentanoate	Generator, HMDB

Chemical Formula

C₅H₁₁NO₂

Average Molecular Weight

117.1463

Monoisotopic Molecular Weight

117.078978601

IUPAC Name

5-aminopentanoic acid

Traditional Name

5-aminovaleric acid

CAS Registry Number

660-88-8

SMILES

NCCCCC(O)=O

InChI Identifier

InChI=1S/C5H11NO2/c6-4-2-1-3-5(7)8/h1-4,6H2,(H,7,8)

InChI Key

JJMDCOVWQOJGCB-UHFFFAOYSA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as delta amino acids and derivatives. Delta amino acids and derivatives are compounds containing a carboxylic acid group and an amino group at the C5 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

Delta amino acids and derivatives

Alternative Parents

Substituents

Delta amino acid or derivatives
Straight chain fatty acid
Fatty acid
Fatty acyl
Amino acid
Carboxylic acid
Monocarboxylic acid or derivatives
Amine
Hydrocarbon derivative
Organic oxide
Primary amine
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Primary aliphatic amine
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

omega-amino fatty acid (CHEBI:15887 )
delta-amino acid (CHEBI:15887 )
Amino fatty acids (C00431 )
Amino fatty acids (LMFA01100040 )

Ontology

Status

Detected but not Quantified

Origin

Not Available

Biofunction

Not Available

Application

Not Available

Cellular locations

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	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	-2.8	ALOGPS
logP	-2.4	ChemAxon
logS	0.24	ALOGPS
pKa (Strongest Acidic)	4.65	ChemAxon
pKa (Strongest Basic)	10.21	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	63.32 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	30.06 m³·mol⁻¹	ChemAxon
Polarizability	12.65 Å³	ChemAxon
Number of Rings	0	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	View
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-00di-1900000000-37b43ab4ca79d55eaf25	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-00fr-3910000000-9345963250dd5bb94624	Spectrum
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-0536-9000000000-5adf6445ea3955b657bd	Spectrum
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-00di-0910000000-74bd5c8746b39b3c0420	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-1900000000-37b43ab4ca79d55eaf25	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-00fr-3910000000-9345963250dd5bb94624	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-1900000000-f11968cc499179c1c6dc	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00dr-4900000000-3ea14dbac57e0143438f	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0fe0-4920000000-3f3f703bde631395004a	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-001i-9000000000-4e782590c46224696321	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-0fk9-9700000000-88ec0b1d4be9919f59a4	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0udi-1900000000-2defcb7a4884b3297cac	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-0f89-9500000000-5fd8b1ba2492405b08ef	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0gb9-3900000000-0afcdbe5370c811ffcaa	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-014i-0900000000-7ac1f98cc9b9752a76d6	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-014i-0900000000-f5c899766b4d912df5ce	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-014i-0900000000-5e5ee374be357b4e26a4	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-0gb9-0900000000-969dd1eb59619aa0cf7a	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-0zfr-9700000000-fe04f26630dfb11c0ca0	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-0a4i-9000000000-fe2ccbb2c7e8d2912ff5	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-0a4i-9000000000-58e7344ed5410bdb1ae7	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive	splash10-0a4i-9000000000-3f1c0f186d2397481f21	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-0udi-1900000000-17b2a3b2a8a744b197fc	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-014i-0900000000-dfd5e0188b9d032c50c5	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-014i-0900000000-7ac1f98cc9b9752a76d6	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-014i-0900000000-f5c899766b4d912df5ce	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-014i-0900000000-5e5ee374be357b4e26a4	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-014i-0900000000-dfd5e0188b9d032c50c5	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-0gb9-0900000000-969dd1eb59619aa0cf7a	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-0zfr-9700000000-fe04f26630dfb11c0ca0	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-2900000000-36fcf52a7600d383116c	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0zgi-9600000000-e0d24cc72e765633ef93	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4l-9000000000-177c4dd0230c5c481274	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-4900000000-50c9e3e40bbc639d1f2e	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01ba-9500000000-f55ea028ca0fae6c620b	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9000000000-83bf020782f77c2d4ef7	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	Spectrum

Biological Properties

Cellular Locations

Not Available

Biofluid Locations and Tissue Locations

Feces
Plasma
Ruminal Fluid
Serum

Concentrations

Biofluid	Status	Value	Condition	Species	Reference	Details
Feces	Detected but not Quantified	Not Applicable	Not Available	Equine	E. E. Escalona, J...	details
Feces	Detected but not Quantified	Not Applicable	Not Available	Ovine	17249687	details
Plasma	Detected but not Quantified	Not Applicable	Not Available	Ovine	17249687	details
Ruminal Fluid	Detected but not Quantified	Not Applicable	Not Available	Bovine	25599412	details
Serum	Detected but not Quantified	Not Applicable	Not Available	Caprine	24214495	details

External Links

DrugBank ID

Not Available

HMDB ID

HMDB0003355

FooDB ID

FDB023151

Phenol Explorer ID

Not Available

KNApSAcK ID

C00052162

BiGG ID

Not Available

BioCyc ID

5-AMINOPENTANOATE

METLIN ID

6902

PDB ID

Not Available

Wikipedia Link

Not Available

Chemspider ID

ChEBI ID

PubChem Compound ID

Kegg Compound ID

YMDB ID

Not Available

ECMDB ID

M2MDB005341

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Fothergill JC, Guest JR: Catabolism of L-lysine by Pseudomonas aeruginosa. J Gen Microbiol. 1977 Mar;99(1):139-55. [405455 ]
Callery PS, Geelhaar LA: Biosynthesis of 5-aminopentanoic acid and 2-piperidone from cadaverine and 1-piperideine in mouse. J Neurochem. 1984 Dec;43(6):1631-4. [6436440 ]
Syrjanen S, Piironen P, Markkanen H: Free amino-acid content of wax-stimulated human whole saliva as related to periodontal disease. Arch Oral Biol. 1987;32(9):607-10. [3481959 ]
Callery PS, Geelhaar LA: 1-Piperideine as an in vivo precursor of the gamma-aminobutyric acid homologue 5-aminopentanoic acid. J Neurochem. 1985 Sep;45(3):946-8. [4031870 ]
Cole KR, Castellino FJ: The binding of antifibrinolytic amino acids to kringle-4-containing fragments of plasminogen. Arch Biochem Biophys. 1984 Mar;229(2):568-75. [6703712 ]

Showing metabocard for 5-Aminopentanoic acid (LMDB00429)

Structure for LMDB00429 (5-Aminopentanoic acid)