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Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2006-08-12 19:17:39 UTC

Update Date

2023-02-21 17:16:37 UTC

HMDB ID

HMDB0003355

Secondary Accession Numbers

HMDB03355

Metabolite Identification

Common Name

5-Aminopentanoic acid

Description

5-Aminopentanoic acid (or 5-aminovalerate) 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 human 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- aminovalerate is an in vivo substrate of 4-aminobutyrate:2-oxoglutarate aminotransferase (PMID:4031870 ). It can be found in Corynebacterium (PMID:27717386 ).

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

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

Physiological effect

Health effect

Intervention

Periodontal Probing Depth (HMDB: HMDB0003355)

Observation

Supragingival Calculus (HMDB: HMDB0003355)
Supragingival Plaque (HMDB: HMDB0003355)

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 32966057)
Saliva (PMID: 22308371)

Organ

Liver (HMDB: HMDB0003355)

Excreta

Biofluid or Excreta

Urine (PMID: 19309105)
Feces (PMID: 20669995)

Cellular substructure

Cytoplasm (HMDB: HMDB0003355)

Source

Endogenous

Endogenous (HMDB: HMDB0003355)

Microbe

Microbe (HMDB: HMDB0003355)
Corynebacterium glutamicum (HMDB: HMDB0003355)

Exogenous

Exogenous (HMDB: HMDB0003355)

Food

Animal origin

Poultry

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Milk and milk product

Unfermented milk

Milk (Cow) (FooDB: FOOD00618)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	157.5 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	1000 mg/mL at 20 °C	Not Available
LogP	-2.63	HANSCH,C ET AL. (1995)

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M-H]-	MetCCS_train_neg	124.492	30932474
[M+H]+	MetCCS_train_pos	121.274	30932474
[M-H]-	Not Available	124.492	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000056
[M+H]+	Not Available	121.708	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000056

Predicted Molecular Properties

Property	Value	Source
Water Solubility	206 g/L	ALOGPS
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	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]+	124.995	31661259
DarkChem	[M-H]-	119.964	31661259
DeepCCS	[M+H]+	139.196	30932474
DeepCCS	[M-H]-	136.436	30932474
DeepCCS	[M-2H]-	172.831	30932474
DeepCCS	[M+Na]+	147.504	30932474
AllCCS	[M+H]+	127.6	32859911
AllCCS	[M+H-H2O]+	123.4	32859911
AllCCS	[M+NH4]+	131.5	32859911
AllCCS	[M+Na]+	132.6	32859911
AllCCS	[M-H]-	126.6	32859911
AllCCS	[M+Na-2H]-	129.8	32859911
AllCCS	[M+HCOO]-	133.4	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5-Aminopentanoic acid	NCCCCC(O)=O	2024.2	Standard polar	33892256
5-Aminopentanoic acid	NCCCCC(O)=O	1192.0	Standard non polar	33892256
5-Aminopentanoic acid	NCCCCC(O)=O	1134.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5-Aminopentanoic acid,1TMS,isomer #1	C[Si](C)(C)OC(=O)CCCCN	1221.1	Semi standard non polar	33892256
5-Aminopentanoic acid,1TMS,isomer #2	C[Si](C)(C)NCCCCC(=O)O	1350.5	Semi standard non polar	33892256
5-Aminopentanoic acid,2TMS,isomer #1	C[Si](C)(C)NCCCCC(=O)O[Si](C)(C)C	1390.2	Semi standard non polar	33892256
5-Aminopentanoic acid,2TMS,isomer #1	C[Si](C)(C)NCCCCC(=O)O[Si](C)(C)C	1490.7	Standard non polar	33892256
5-Aminopentanoic acid,2TMS,isomer #1	C[Si](C)(C)NCCCCC(=O)O[Si](C)(C)C	1539.6	Standard polar	33892256
5-Aminopentanoic acid,2TMS,isomer #2	C[Si](C)(C)N(CCCCC(=O)O)[Si](C)(C)C	1580.3	Semi standard non polar	33892256
5-Aminopentanoic acid,2TMS,isomer #2	C[Si](C)(C)N(CCCCC(=O)O)[Si](C)(C)C	1524.2	Standard non polar	33892256
5-Aminopentanoic acid,2TMS,isomer #2	C[Si](C)(C)N(CCCCC(=O)O)[Si](C)(C)C	1788.9	Standard polar	33892256
5-Aminopentanoic acid,3TMS,isomer #1	C[Si](C)(C)OC(=O)CCCCN([Si](C)(C)C)[Si](C)(C)C	1641.4	Semi standard non polar	33892256
5-Aminopentanoic acid,3TMS,isomer #1	C[Si](C)(C)OC(=O)CCCCN([Si](C)(C)C)[Si](C)(C)C	1614.2	Standard non polar	33892256
5-Aminopentanoic acid,3TMS,isomer #1	C[Si](C)(C)OC(=O)CCCCN([Si](C)(C)C)[Si](C)(C)C	1541.5	Standard polar	33892256
5-Aminopentanoic acid,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CCCCN	1441.4	Semi standard non polar	33892256
5-Aminopentanoic acid,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NCCCCC(=O)O	1601.5	Semi standard non polar	33892256
5-Aminopentanoic acid,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NCCCCC(=O)O[Si](C)(C)C(C)(C)C	1861.5	Semi standard non polar	33892256
5-Aminopentanoic acid,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NCCCCC(=O)O[Si](C)(C)C(C)(C)C	1856.7	Standard non polar	33892256
5-Aminopentanoic acid,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NCCCCC(=O)O[Si](C)(C)C(C)(C)C	1792.8	Standard polar	33892256
5-Aminopentanoic acid,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(CCCCC(=O)O)[Si](C)(C)C(C)(C)C	2004.5	Semi standard non polar	33892256
5-Aminopentanoic acid,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(CCCCC(=O)O)[Si](C)(C)C(C)(C)C	1920.2	Standard non polar	33892256
5-Aminopentanoic acid,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(CCCCC(=O)O)[Si](C)(C)C(C)(C)C	1930.8	Standard polar	33892256
5-Aminopentanoic acid,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2279.4	Semi standard non polar	33892256
5-Aminopentanoic acid,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2189.5	Standard non polar	33892256
5-Aminopentanoic acid,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	1920.7	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - 5-Aminopentanoic acid GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-00di-1900000000-37b43ab4ca79d55eaf25	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 5-Aminopentanoic acid GC-MS (3 TMS)	splash10-00fr-3910000000-9345963250dd5bb94624	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 5-Aminopentanoic acid EI-B (Non-derivatized)	splash10-0536-9000000000-5adf6445ea3955b657bd	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 5-Aminopentanoic acid EI-B (Non-derivatized)	splash10-00di-0910000000-74bd5c8746b39b3c0420	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 5-Aminopentanoic acid GC-EI-TOF (Non-derivatized)	splash10-00di-1900000000-37b43ab4ca79d55eaf25	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 5-Aminopentanoic acid GC-MS (Non-derivatized)	splash10-00fr-3910000000-9345963250dd5bb94624	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 5-Aminopentanoic acid GC-EI-TOF (Non-derivatized)	splash10-00di-1900000000-f11968cc499179c1c6dc	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 5-Aminopentanoic acid GC-EI-TOF (Non-derivatized)	splash10-00dr-4900000000-3ea14dbac57e0143438f	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 5-Aminopentanoic acid GC-EI-TOF (Non-derivatized)	splash10-0fe0-4920000000-3f3f703bde631395004a	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Aminopentanoic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-001i-9000000000-4e782590c46224696321	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Aminopentanoic acid GC-MS (1 TMS) - 70eV, Positive	splash10-0fk9-9700000000-88ec0b1d4be9919f59a4	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Aminopentanoic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Aminopentanoic 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 - 5-Aminopentanoic acid Quattro_QQQ 10V, Positive-QTOF (Annotated)	splash10-0udi-1900000000-2defcb7a4884b3297cac	2012-07-25	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Aminopentanoic acid Quattro_QQQ 25V, Positive-QTOF (Annotated)	splash10-0f89-9500000000-5fd8b1ba2492405b08ef	2012-07-25	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Aminopentanoic acid Quattro_QQQ 40V, Positive-QTOF (Annotated)	splash10-0gb9-3900000000-0afcdbe5370c811ffcaa	2012-07-25	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Aminopentanoic acid LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative-QTOF	splash10-014i-0900000000-7ac1f98cc9b9752a76d6	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Aminopentanoic acid LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative-QTOF	splash10-014i-0900000000-f5c899766b4d912df5ce	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Aminopentanoic acid LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative-QTOF	splash10-014i-0900000000-5e5ee374be357b4e26a4	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Aminopentanoic acid LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive-QTOF	splash10-0gb9-0900000000-969dd1eb59619aa0cf7a	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Aminopentanoic acid LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive-QTOF	splash10-0zfr-9700000000-fe04f26630dfb11c0ca0	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Aminopentanoic acid LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive-QTOF	splash10-0a4i-9000000000-fe2ccbb2c7e8d2912ff5	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Aminopentanoic acid LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive-QTOF	splash10-0a4i-9000000000-58e7344ed5410bdb1ae7	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Aminopentanoic acid LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive-QTOF	splash10-0a4i-9000000000-3f1c0f186d2397481f21	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Aminopentanoic acid LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive-QTOF	splash10-0udi-1900000000-17b2a3b2a8a744b197fc	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Aminopentanoic acid LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative-QTOF	splash10-014i-0900000000-dfd5e0188b9d032c50c5	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Aminopentanoic acid LC-ESI-QQ , negative-QTOF	splash10-014i-0900000000-7ac1f98cc9b9752a76d6	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Aminopentanoic acid LC-ESI-QQ , negative-QTOF	splash10-014i-0900000000-f5c899766b4d912df5ce	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Aminopentanoic acid LC-ESI-QQ , negative-QTOF	splash10-014i-0900000000-5e5ee374be357b4e26a4	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Aminopentanoic acid LC-ESI-QTOF , negative-QTOF	splash10-014i-0900000000-dfd5e0188b9d032c50c5	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Aminopentanoic acid LC-ESI-QQ , positive-QTOF	splash10-0gb9-0900000000-969dd1eb59619aa0cf7a	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Aminopentanoic acid LC-ESI-QQ , positive-QTOF	splash10-0zfr-9700000000-fe04f26630dfb11c0ca0	2017-09-14	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Aminopentanoic acid 10V, Positive-QTOF	splash10-0udi-2900000000-36fcf52a7600d383116c	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Aminopentanoic acid 20V, Positive-QTOF	splash10-0zgi-9600000000-e0d24cc72e765633ef93	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Aminopentanoic acid 40V, Positive-QTOF	splash10-0a4l-9000000000-177c4dd0230c5c481274	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Aminopentanoic acid 10V, Negative-QTOF	splash10-014i-4900000000-50c9e3e40bbc639d1f2e	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Aminopentanoic acid 20V, Negative-QTOF	splash10-01ba-9500000000-f55ea028ca0fae6c620b	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Aminopentanoic acid 40V, Negative-QTOF	splash10-0a4l-9000000000-83bf020782f77c2d4ef7	2017-09-01	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Experimental 1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	2012-12-05	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Experimental 2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	2012-12-05	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm (predicted from logP)

Biospecimen Locations

Blood
Feces
Saliva
Urine

Tissue Locations

Liver

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details
Blood	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	32966057	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	21761941	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	25037050	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	27543620	details
Feces	Detected but not Quantified	Not Quantified	Infant (0-1 year old)	Not Specified	Normal	24628373	details
Feces	Detected but not Quantified	Not Quantified	Infant (0-1 year old)	Not Specified	Normal	24628373	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	29808030	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	18052033	details
Feces	Detected but not Quantified	Not Quantified	Infant (0-1 year old)	Not Available	Normal	24628373	details
Feces	Detected but not Quantified	Not Quantified	Infant (0-1 year old)	Both	Normal	24375085	details
Feces	Detected and Quantified	262.0655 +/- 254.383 nmol/g wet feces	Not Specified	Not Specified	Normal	20669995	details
Feces	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	20669995	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	28842642	details
Saliva	Detected and Quantified	74.2 +/- 1.05×102 uM	Adult (>18 years old)	Not Specified	Normal	Sugimoto et al. (...	details
Saliva	Detected and Quantified	119 +/- 93.3 uM	Adult (>18 years old)	Not Specified	Normal	Sugimoto et al. (...	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected and Quantified	470.38 +/- 342.79 uM	Adult (>18 years old)	Both	Normal	Zerihun T. Dame, ...	details
Urine	Detected and Quantified	0.10 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	19309105	details
Urine	Detected and Quantified	1.0-1.2 umol/mmol creatinine	Adult (>18 years old)	Female	Normal	27012787	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	21389975	details
Urine	Detected and Quantified	0.98-1.2 umol/mmol creatinine	Adult (>18 years old)	Male	Normal	27012787	details
Urine	Detected and Quantified	2 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	21388201	details
Urine	Detected and Quantified	1.1 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	24023812	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Irritable bowel syndrome	21761941	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Ulcerative colitis	21761941	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal cancer	27015276	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal cancer	25037050	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Ulcerative colitis	28842642	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal Cancer	27275383	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Periodontal Probing Depth	31026179	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Supragingival Calculus	31026179	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Supragingival Plaque	31026179	details

Associated Disorders and Diseases

Disease References

Irritable bowel syndrome
Le Gall G, Noor SO, Ridgway K, Scovell L, Jamieson C, Johnson IT, Colquhoun IJ, Kemsley EK, Narbad A: Metabolomics of fecal extracts detects altered metabolic activity of gut microbiota in ulcerative colitis and irritable bowel syndrome. J Proteome Res. 2011 Sep 2;10(9):4208-18. doi: 10.1021/pr2003598. Epub 2011 Aug 8. [PubMed:21761941 ]
Ulcerative colitis
Le Gall G, Noor SO, Ridgway K, Scovell L, Jamieson C, Johnson IT, Colquhoun IJ, Kemsley EK, Narbad A: Metabolomics of fecal extracts detects altered metabolic activity of gut microbiota in ulcerative colitis and irritable bowel syndrome. J Proteome Res. 2011 Sep 2;10(9):4208-18. doi: 10.1021/pr2003598. Epub 2011 Aug 8. [PubMed:21761941 ] Azario I, Pievani A, Del Priore F, Antolini L, Santi L, Corsi A, Cardinale L, Sawamoto K, Kubaski F, Gentner B, Bernardo ME, Valsecchi MG, Riminucci M, Tomatsu S, Aiuti A, Biondi A, Serafini M: Neonatal umbilical cord blood transplantation halts skeletal disease progression in the murine model of MPS-I. Sci Rep. 2017 Aug 25;7(1):9473. doi: 10.1038/s41598-017-09958-9. [PubMed:28842642 ]
Colorectal cancer
Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ] Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ] Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Periodontal Probing Depth
Liebsch C, Pitchika V, Pink C, Samietz S, Kastenmuller G, Artati A, Suhre K, Adamski J, Nauck M, Volzke H, Friedrich N, Kocher T, Holtfreter B, Pietzner M: The Saliva Metabolome in Association to Oral Health Status. J Dent Res. 2019 Jun;98(6):642-651. doi: 10.1177/0022034519842853. Epub 2019 Apr 26. [PubMed:31026179 ]
Supragingival Calculus
Liebsch C, Pitchika V, Pink C, Samietz S, Kastenmuller G, Artati A, Suhre K, Adamski J, Nauck M, Volzke H, Friedrich N, Kocher T, Holtfreter B, Pietzner M: The Saliva Metabolome in Association to Oral Health Status. J Dent Res. 2019 Jun;98(6):642-651. doi: 10.1177/0022034519842853. Epub 2019 Apr 26. [PubMed:31026179 ]
Supragingival Plaque
Liebsch C, Pitchika V, Pink C, Samietz S, Kastenmuller G, Artati A, Suhre K, Adamski J, Nauck M, Volzke H, Friedrich N, Kocher T, Holtfreter B, Pietzner M: The Saliva Metabolome in Association to Oral Health Status. J Dent Res. 2019 Jun;98(6):642-651. doi: 10.1177/0022034519842853. Epub 2019 Apr 26. [PubMed:31026179 ]

Associated OMIM IDs

114500 (Colorectal cancer)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

6902

PubChem Compound

138

PDB ID

Not Available

ChEBI ID

15887

Food Biomarker Ontology

Not Available

VMH ID

5APTN

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Allan, Robin D.; Dickenson, Helena W.; Johnston, Graham A. R.; Kazlauskas, Rymantas; Tran, Hue W. Synthesis of analogs of GABA. XIV. Synthesis and activity of unsaturated derivatives of 5-aminopentanoic acid (d-aminovaleric acid). Australian Journal of Chemistry (1985), 38(11), 1651-6.

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

Santos A, Zanetta S, Cresteil T, Deroussent A, Pein F, Raymond E, Vernillet L, Risse ML, Boige V, Gouyette A, Vassal G: Metabolism of irinotecan (CPT-11) by CYP3A4 and CYP3A5 in humans. Clin Cancer Res. 2000 May;6(5):2012-20. [PubMed:10815927 ]
Sparreboom A, de Jonge MJ, de Bruijn P, Brouwer E, Nooter K, Loos WJ, van Alphen RJ, Mathijssen RH, Stoter G, Verweij J: Irinotecan (CPT-11) metabolism and disposition in cancer patients. Clin Cancer Res. 1998 Nov;4(11):2747-54. [PubMed:9829738 ]
Fujita K, Ando Y, Narabayashi M, Miya T, Nagashima F, Yamamoto W, Kodama K, Araki K, Endo H, Sasaki Y: Gefitinib (Iressa) inhibits the CYP3A4-mediated formation of 7-ethyl-10-(4-amino-1-piperidino)carbonyloxycamptothecin but activates that of 7-ethyl-10-[4-N-(5-aminopentanoic acid)-1-piperidino]carbonyloxycamptothecin from irinotecan. Drug Metab Dispos. 2005 Dec;33(12):1785-90. Epub 2005 Aug 25. [PubMed:16123050 ]
Poujol S, Pinguet F, Malosse F, Astre C, Ychou M, Culine S, Bressolle F: Sensitive HPLC-fluorescence method for irinotecan and four major metabolites in human plasma and saliva: application to pharmacokinetic studies. Clin Chem. 2003 Nov;49(11):1900-8. [PubMed:14578322 ]
van den Berg GA, Nagel GT, Muskiet FA, Halie MR: Mass fragmentographic identification of polyamine metabolites in the urine of normal persons and cancer patients, and its relevance to the use of polyamines as tumour markers. J Chromatogr. 1985 May 3;339(2):223-31. [PubMed:4008565 ]
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. [PubMed:3481959 ]
Fothergill JC, Guest JR: Catabolism of L-lysine by Pseudomonas aeruginosa. J Gen Microbiol. 1977 Mar;99(1):139-55. [PubMed: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. [PubMed:6436440 ]
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. [PubMed: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. [PubMed:6703712 ]
Shin JH, Park SH, Oh YH, Choi JW, Lee MH, Cho JS, Jeong KJ, Joo JC, Yu J, Park SJ, Lee SY: Metabolic engineering of Corynebacterium glutamicum for enhanced production of 5-aminovaleric acid. Microb Cell Fact. 2016 Oct 7;15(1):174. doi: 10.1186/s12934-016-0566-8. [PubMed:27717386 ]

Showing metabocard for 5-Aminopentanoic acid (HMDB0003355)

MOL for HMDB0003355 (5-Aminopentanoic acid)

3D MOL for HMDB0003355 (5-Aminopentanoic acid)

3D SDF for HMDB0003355 (5-Aminopentanoic acid)

3D-SDF for HMDB0003355 (5-Aminopentanoic acid)

PDB for HMDB0003355 (5-Aminopentanoic acid)

3D PDB for HMDB0003355 (5-Aminopentanoic acid)

SMILES for HMDB0003355 (5-Aminopentanoic acid)

INCHI for HMDB0003355 (5-Aminopentanoic acid)

Structure for HMDB0003355 (5-Aminopentanoic acid)

3D Structure for HMDB0003355 (5-Aminopentanoic acid)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra