Jump To Section:

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

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 23:41:22 UTC

Update Date

2021-09-26 23:18:06 UTC

HMDB ID

HMDB0260147

Secondary Accession Numbers

None

Metabolite Identification

Common Name

(2S)-6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid

Description

(2S)-6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof. Based on a literature review very few articles have been published on (2S)-6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). (2s)-6-oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically (2S)-6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic 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
(2S)-6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylate	Generator
6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylate	HMDB

Chemical Formula

C₅H₇NO₃

Average Molecular Weight

129.115

Monoisotopic Molecular Weight

129.042593089

IUPAC Name

6-oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid

Traditional Name

6-oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

OC(=O)C1CCC2ON12

InChI Identifier

InChI=1S/C5H7NO3/c7-5(8)3-1-2-4-6(3)9-4/h3-4H,1-2H2,(H,7,8)

InChI Key

GBYVFZVPFPPNDL-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.

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 and derivatives

Alternative Parents

Substituents

Alpha-amino acid or derivatives
Pyrrolidine carboxylic acid
Pyrrolidine carboxylic acid or derivatives
1,2-oxazinane
Oxazinane
Pyrrolidine
Carboxylic acid
Monocarboxylic acid or derivatives
Oxacycle
Azacycle
Organoheterocyclic compound
N-organohydroxylamine
Organooxygen compound
Organonitrogen compound
Organic oxide
Hydrocarbon derivative
Organic oxygen compound
Carbonyl group
Organic nitrogen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic 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	-1.8	ALOGPS
logP	-0.18	ChemAxon
logS	1.05	ALOGPS
pKa (Strongest Acidic)	3.74	ChemAxon
pKa (Strongest Basic)	-4.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	52.84 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	27.19 m³·mol⁻¹	ChemAxon
Polarizability	11.47 Å³	ChemAxon
Number of Rings	2	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
AllCCS	[M+H]+	127.241	32859911
AllCCS	[M+H-H2O]+	122.517	32859911
AllCCS	[M+Na]+	132.922	32859911
AllCCS	[M+NH4]+	131.65	32859911
AllCCS	[M-H]-	121.323	32859911
AllCCS	[M+Na-2H]-	122.857	32859911
AllCCS	[M+HCOO]-	124.59	32859911
DeepCCS	[M-2H]-	157.465	30932474
DeepCCS	[M+Na]+	132.118	30932474

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. Predicted by Afia on May 17, 2022.	2.43 minutes	32390414
Predicted by Siyang on May 30, 2022	10.5696 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.88 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1285.5 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	358.8 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	101.8 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	225.6 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	86.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	315.6 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	373.3 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	220.5 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	764.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	254.9 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	1036.3 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	235.5 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	263.0 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	672.0 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	277.4 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	262.6 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(2S)-6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid	OC(=O)C1CCC2ON12	2131.1	Standard polar	33892256
(2S)-6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid	OC(=O)C1CCC2ON12	1138.7	Standard non polar	33892256
(2S)-6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid	OC(=O)C1CCC2ON12	1242.4	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - (2S)-6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-0560-9000000000-59d0429974400fc28981	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (2S)-6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (2S)-6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (2S)-6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-27	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

53830296

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 (2S)-6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid (HMDB0260147)

MOL for HMDB0260147 ((2S)-6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid)

3D MOL for HMDB0260147 ((2S)-6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid)

3D SDF for HMDB0260147 ((2S)-6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid)

3D-SDF for HMDB0260147 ((2S)-6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid)

PDB for HMDB0260147 ((2S)-6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid)

3D PDB for HMDB0260147 ((2S)-6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid)

SMILES for HMDB0260147 ((2S)-6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid)

INCHI for HMDB0260147 ((2S)-6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid)

Structure for HMDB0260147 ((2S)-6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid)

3D Structure for HMDB0260147 ((2S)-6-Oxa-1-azabicyclo[3.1.0]hexane-2-carboxylic acid)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

NMR Spectra