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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 01:35:13 UTC

Update Date

2023-02-21 17:27:28 UTC

HMDB ID

HMDB0040040

Secondary Accession Numbers

HMDB40040

Metabolite Identification

Common Name

5H-Cyclopentapyrazine

Description

5H-Cyclopentapyrazine belongs to the class of organic compounds known as pyrazines. Pyrazines are compounds containing a pyrazine ring, which is a six-member aromatic heterocycle, that consists of two nitrogen atoms (at positions 1 and 4) and four carbon atoms. 5H-Cyclopentapyrazine has been detected, but not quantified in, pulses. This could make 5H-cyclopentapyrazine a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 5H-Cyclopentapyrazine.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₇H₆N₂

Average Molecular Weight

118.1359

Monoisotopic Molecular Weight

118.053098202

IUPAC Name

5H-cyclopenta[b]pyrazine

Traditional Name

5H-cyclopenta[b]pyrazine

CAS Registry Number

25042-83-5

SMILES

C1C=CC2=C1N=CC=N2

InChI Identifier

InChI=1S/C7H6N2/c1-2-6-7(3-1)9-5-4-8-6/h1-2,4-5H,3H2

InChI Key

RNVGIKWJGFOBOF-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrazines. Pyrazines are compounds containing a pyrazine ring, which is a six-member aromatic heterocycle, that consists of two nitrogen atoms (at positions 1 and 4) and four carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrazines

Direct Parent

Pyrazines

Alternative Parents

Substituents

Pyrazine
Heteroaromatic compound
Azacycle
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0040040)
Cytoplasm (HMDB: HMDB0040040)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0040040)

Source

Exogenous

Exogenous (HMDB: HMDB0040040)

Food

Food (HMDB: HMDB0040040)

Pulse

Pulses (FooDB: FOOD00867)

Endogenous

Plant

Fabaceae (HMDB: HMDB0040040)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0040040)

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	9657 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	96.9 g/L	ALOGPS
logP	0.88	ALOGPS
logP	0.37	ChemAxon
logS	-0.09	ALOGPS
pKa (Strongest Acidic)	10.46	ChemAxon
pKa (Strongest Basic)	0.49	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	25.78 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	34.87 m³·mol⁻¹	ChemAxon
Polarizability	12.16 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	122.435	30932474
DeepCCS	[M-H]-	119.39	30932474
DeepCCS	[M-2H]-	156.182	30932474
DeepCCS	[M+Na]+	130.999	30932474
AllCCS	[M+H]+	125.1	32859911
AllCCS	[M+H-H2O]+	120.2	32859911
AllCCS	[M+NH4]+	129.7	32859911
AllCCS	[M+Na]+	131.1	32859911
AllCCS	[M-H]-	120.8	32859911
AllCCS	[M+Na-2H]-	122.4	32859911
AllCCS	[M+HCOO]-	124.2	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. Predicted by Afia on May 17, 2022.	2.4 minutes	32390414
Predicted by Siyang on May 30, 2022	8.818 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.72 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	105.5 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	682.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	336.4 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	119.8 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	241.3 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	75.5 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	286.8 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	287.4 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	415.6 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	715.9 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	41.8 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	804.1 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	205.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	254.4 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	539.3 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	396.3 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	104.4 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5H-Cyclopentapyrazine	C1C=CC2=C1N=CC=N2	1703.7	Standard polar	33892256
5H-Cyclopentapyrazine	C1C=CC2=C1N=CC=N2	1072.4	Standard non polar	33892256
5H-Cyclopentapyrazine	C1C=CC2=C1N=CC=N2	1118.9	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 - 5H-Cyclopentapyrazine GC-MS (Non-derivatized) - 70eV, Positive	splash10-014i-5900000000-a4ae84be2d4a96a61af9	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5H-Cyclopentapyrazine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5H-Cyclopentapyrazine 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 - 5H-Cyclopentapyrazine 10V, Positive-QTOF	splash10-014i-0900000000-8d02c9677431676d6d9a	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5H-Cyclopentapyrazine 20V, Positive-QTOF	splash10-014i-0900000000-06a2f26a90e2ad219b70	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5H-Cyclopentapyrazine 40V, Positive-QTOF	splash10-0gbl-9600000000-f50b0b06d80dd2c2f394	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5H-Cyclopentapyrazine 10V, Negative-QTOF	splash10-014i-0900000000-349a4a77b4aafe4a83ae	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5H-Cyclopentapyrazine 20V, Negative-QTOF	splash10-014i-0900000000-349a4a77b4aafe4a83ae	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5H-Cyclopentapyrazine 40V, Negative-QTOF	splash10-014i-0900000000-5d0c6720b7f1a37b198b	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5H-Cyclopentapyrazine 10V, Negative-QTOF	splash10-014i-0900000000-6e1aa709126082eacb98	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5H-Cyclopentapyrazine 20V, Negative-QTOF	splash10-014i-0900000000-6e1aa709126082eacb98	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5H-Cyclopentapyrazine 40V, Negative-QTOF	splash10-014i-0900000000-6e1aa709126082eacb98	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5H-Cyclopentapyrazine 10V, Positive-QTOF	splash10-014i-0900000000-b264926dd01c80902ad8	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5H-Cyclopentapyrazine 20V, Positive-QTOF	splash10-014i-0900000000-d6f37af903b3b9add466	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5H-Cyclopentapyrazine 40V, Positive-QTOF	splash10-00kf-9500000000-b95eb77943134f6d83af	2021-09-23	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	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]+)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-04	FELIX 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

FDB019727

KNApSAcK ID

C00054445

Chemspider ID

16148443

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

12306192

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1630561

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 5H-Cyclopentapyrazine (HMDB0040040)

MOL for HMDB0040040 (5H-Cyclopentapyrazine)

3D MOL for HMDB0040040 (5H-Cyclopentapyrazine)

3D SDF for HMDB0040040 (5H-Cyclopentapyrazine)

3D-SDF for HMDB0040040 (5H-Cyclopentapyrazine)

PDB for HMDB0040040 (5H-Cyclopentapyrazine)

3D PDB for HMDB0040040 (5H-Cyclopentapyrazine)

SMILES for HMDB0040040 (5H-Cyclopentapyrazine)

INCHI for HMDB0040040 (5H-Cyclopentapyrazine)

Structure for HMDB0040040 (5H-Cyclopentapyrazine)

3D Structure for HMDB0040040 (5H-Cyclopentapyrazine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra