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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-08-29 22:59:08 UTC

Update Date

2021-09-26 22:48:56 UTC

HMDB ID

HMDB0242326

Secondary Accession Numbers

None

Metabolite Identification

Common Name

(1r,2s)-2-Aminocyclopentanecarboxylic acid

Description

(1r,2s)-2-Aminocyclopentanecarboxylic acid, also known as cispentacin or 2-aminocyclopentane-1-carboxylate, belongs to the class of organic compounds known as beta amino acids and derivatives. These are amino acids having a (-NH2) group attached to the beta carbon atom. Based on a literature review very few articles have been published on (1r,2s)-2-Aminocyclopentanecarboxylic acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). (1r,2s)-2-aminocyclopentanecarboxylic acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically (1r,2s)-2-Aminocyclopentanecarboxylic acid is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
(1R,2S)-2-Aminocyclopentanecarboxylate	Generator
2-Aminocyclopentane-1-carboxylate	HMDB
Cispentacin	HMDB
Cispentacin, carboxy-(11)C-labeled	HMDB
trans-ACPC	HMDB
cis-2-Ac5c	HMDB
Cispentacin tosylate	HMDB
Cispentacin, monopotassium salt, (cis)-isomer	HMDB
Cispentacin, monosodium salt, (cis)-isomer	HMDB
Cispentacin, (cis-(+-))-isomer	HMDB
Cispentacin, (trans-(+-))-isomer	HMDB
Cispentacin, (cis)-isomer	HMDB

Chemical Formula

C₆H₁₁NO₂

Average Molecular Weight

129.159

Monoisotopic Molecular Weight

129.078978598

IUPAC Name

2-aminocyclopentane-1-carboxylic acid

Traditional Name

2-aminocyclopentane-1-carboxylic acid

CAS Registry Number

Not Available

SMILES

NC1CCCC1C(O)=O

InChI Identifier

InChI=1S/C6H11NO2/c7-5-3-1-2-4(5)6(8)9/h4-5H,1-3,7H2,(H,8,9)

InChI Key

JWYOAMOZLZXDER-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as beta amino acids and derivatives. These are amino acids having a (-NH2) group attached to the beta 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

Beta amino acids and derivatives

Alternative Parents

Substituents

Beta amino acid or derivatives
Amino acid
Carboxylic acid
Monocarboxylic acid or derivatives
Amine
Organic oxide
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Primary aliphatic amine
Organic oxygen compound
Carbonyl group
Organic nitrogen compound
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular 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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-2.4	ALOGPS
logP	-2.2	ChemAxon
logS	0.22	ALOGPS
pKa (Strongest Acidic)	4.06	ChemAxon
pKa (Strongest Basic)	10.58	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	1	ChemAxon
Refractivity	32.42 m³·mol⁻¹	ChemAxon
Polarizability	13.46 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
DeepCCS	[M+H]+	131.654	30932474
DeepCCS	[M-H]-	128.893	30932474
DeepCCS	[M-2H]-	165.143	30932474
DeepCCS	[M+Na]+	139.968	30932474
AllCCS	[M+H]+	129.5	32859911
AllCCS	[M+H-H2O]+	124.9	32859911
AllCCS	[M+NH4]+	133.7	32859911
AllCCS	[M+Na]+	134.9	32859911
AllCCS	[M-H]-	124.0	32859911
AllCCS	[M+Na-2H]-	126.1	32859911
AllCCS	[M+HCOO]-	128.5	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022.	1.68 minutes	32390414
Predicted by Siyang on May 30, 2022	8.8555 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	5.8 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	547.9 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	295.1 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	63.6 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	178.9 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	71.3 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	255.6 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	234.3 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	757.6 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	589.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	49.5 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	647.6 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	174.0 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	195.9 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	773.1 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	455.9 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	348.3 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(1r,2s)-2-Aminocyclopentanecarboxylic acid	NC1CCCC1C(O)=O	2215.0	Standard polar	33892256
(1r,2s)-2-Aminocyclopentanecarboxylic acid	NC1CCCC1C(O)=O	1194.1	Standard non polar	33892256
(1r,2s)-2-Aminocyclopentanecarboxylic acid	NC1CCCC1C(O)=O	1395.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
(1r,2s)-2-Aminocyclopentanecarboxylic acid,2TMS,isomer #1	C[Si](C)(C)NC1CCCC1C(=O)O[Si](C)(C)C	1431.4	Semi standard non polar	33892256
(1r,2s)-2-Aminocyclopentanecarboxylic acid,2TMS,isomer #1	C[Si](C)(C)NC1CCCC1C(=O)O[Si](C)(C)C	1480.1	Standard non polar	33892256
(1r,2s)-2-Aminocyclopentanecarboxylic acid,2TMS,isomer #1	C[Si](C)(C)NC1CCCC1C(=O)O[Si](C)(C)C	1609.2	Standard polar	33892256
(1r,2s)-2-Aminocyclopentanecarboxylic acid,2TMS,isomer #2	C[Si](C)(C)N(C1CCCC1C(=O)O)[Si](C)(C)C	1640.8	Semi standard non polar	33892256
(1r,2s)-2-Aminocyclopentanecarboxylic acid,2TMS,isomer #2	C[Si](C)(C)N(C1CCCC1C(=O)O)[Si](C)(C)C	1555.3	Standard non polar	33892256
(1r,2s)-2-Aminocyclopentanecarboxylic acid,2TMS,isomer #2	C[Si](C)(C)N(C1CCCC1C(=O)O)[Si](C)(C)C	1946.1	Standard polar	33892256
(1r,2s)-2-Aminocyclopentanecarboxylic acid,3TMS,isomer #1	C[Si](C)(C)OC(=O)C1CCCC1N([Si](C)(C)C)[Si](C)(C)C	1653.6	Semi standard non polar	33892256
(1r,2s)-2-Aminocyclopentanecarboxylic acid,3TMS,isomer #1	C[Si](C)(C)OC(=O)C1CCCC1N([Si](C)(C)C)[Si](C)(C)C	1609.1	Standard non polar	33892256
(1r,2s)-2-Aminocyclopentanecarboxylic acid,3TMS,isomer #1	C[Si](C)(C)OC(=O)C1CCCC1N([Si](C)(C)C)[Si](C)(C)C	1634.9	Standard polar	33892256
(1r,2s)-2-Aminocyclopentanecarboxylic acid,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1CCCC1C(=O)O[Si](C)(C)C(C)(C)C	1895.3	Semi standard non polar	33892256
(1r,2s)-2-Aminocyclopentanecarboxylic acid,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1CCCC1C(=O)O[Si](C)(C)C(C)(C)C	1893.3	Standard non polar	33892256
(1r,2s)-2-Aminocyclopentanecarboxylic acid,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1CCCC1C(=O)O[Si](C)(C)C(C)(C)C	1899.0	Standard polar	33892256
(1r,2s)-2-Aminocyclopentanecarboxylic acid,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C1CCCC1C(=O)O)[Si](C)(C)C(C)(C)C	2074.4	Semi standard non polar	33892256
(1r,2s)-2-Aminocyclopentanecarboxylic acid,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C1CCCC1C(=O)O)[Si](C)(C)C(C)(C)C	2004.5	Standard non polar	33892256
(1r,2s)-2-Aminocyclopentanecarboxylic acid,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C1CCCC1C(=O)O)[Si](C)(C)C(C)(C)C	2077.8	Standard polar	33892256
(1r,2s)-2-Aminocyclopentanecarboxylic acid,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C1CCCC1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2312.0	Semi standard non polar	33892256
(1r,2s)-2-Aminocyclopentanecarboxylic acid,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C1CCCC1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2223.1	Standard non polar	33892256
(1r,2s)-2-Aminocyclopentanecarboxylic acid,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C1CCCC1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2015.6	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - (1r,2s)-2-Aminocyclopentanecarboxylic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-054o-9100000000-6f2a0d05730c54b9ba43	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (1r,2s)-2-Aminocyclopentanecarboxylic 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
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (1r,2s)-2-Aminocyclopentanecarboxylic acid 10V, Positive-QTOF	splash10-001i-9400000000-7808bddfe4a3f4065eec	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (1r,2s)-2-Aminocyclopentanecarboxylic acid 20V, Positive-QTOF	splash10-0159-9200000000-64fa75434fa8d403ef32	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (1r,2s)-2-Aminocyclopentanecarboxylic acid 40V, Positive-QTOF	splash10-05nf-9000000000-321d98ec142988e2b819	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (1r,2s)-2-Aminocyclopentanecarboxylic acid 10V, Negative-QTOF	splash10-004i-0900000000-cd561d3f5ae3eb91c310	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (1r,2s)-2-Aminocyclopentanecarboxylic acid 20V, Negative-QTOF	splash10-0159-9300000000-3c4b38e6e1574231a78b	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (1r,2s)-2-Aminocyclopentanecarboxylic acid 40V, Negative-QTOF	splash10-0a4i-9100000000-16ac14703178966f78c4	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

379990

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

429614

PDB ID

Not Available

ChEBI ID

Not Available

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

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for (1r,2s)-2-Aminocyclopentanecarboxylic acid (HMDB0242326)

MOL for HMDB0242326 ((1r,2s)-2-Aminocyclopentanecarboxylic acid)

3D MOL for HMDB0242326 ((1r,2s)-2-Aminocyclopentanecarboxylic acid)

3D SDF for HMDB0242326 ((1r,2s)-2-Aminocyclopentanecarboxylic acid)

3D-SDF for HMDB0242326 ((1r,2s)-2-Aminocyclopentanecarboxylic acid)

PDB for HMDB0242326 ((1r,2s)-2-Aminocyclopentanecarboxylic acid)

3D PDB for HMDB0242326 ((1r,2s)-2-Aminocyclopentanecarboxylic acid)

SMILES for HMDB0242326 ((1r,2s)-2-Aminocyclopentanecarboxylic acid)

INCHI for HMDB0242326 ((1r,2s)-2-Aminocyclopentanecarboxylic acid)

Structure for HMDB0242326 ((1r,2s)-2-Aminocyclopentanecarboxylic acid)

3D Structure for HMDB0242326 ((1r,2s)-2-Aminocyclopentanecarboxylic acid)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra