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

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 01:22:18 UTC

Update Date

2023-02-21 17:27:13 UTC

HMDB ID

HMDB0039832

Secondary Accession Numbers

HMDB39832

Metabolite Identification

Common Name

6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine

Description

6,7-Dihydro-2,6-dimethyl-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. 6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine has been detected, but not quantified in, a few different foods, such as arabica coffees (Coffea arabica), coffee and coffee products, and robusta coffees (Coffea canephora). This could make 6,7-dihydro-2,6-dimethyl-5H-cyclopentapyrazine a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 6,7-Dihydro-2,6-dimethyl-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

C₉H₁₂N₂

Average Molecular Weight

148.205

Monoisotopic Molecular Weight

148.100048394

IUPAC Name

2,6-dimethyl-5H,6H,7H-cyclopenta[b]pyrazine

Traditional Name

2,6-dimethyl-5H,6H,7H-cyclopenta[b]pyrazine

CAS Registry Number

61928-63-0

SMILES

CC1CC2=C(C1)N=C(C)C=N2

InChI Identifier

InChI=1S/C9H12N2/c1-6-3-8-9(4-6)11-7(2)5-10-8/h5-6H,3-4H2,1-2H3

InChI Key

FKMPZHRHBYPYIZ-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: HMDB0039832)
Cytoplasm (HMDB: HMDB0039832)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0039832)

Source

Exogenous

Food

Food (HMDB: HMDB0039832)

Coffee and coffee product

Coffee

Arabica coffee (FooDB: FOOD00059)
Robusta coffee (FooDB: FOOD00060)

Coffee and coffee products (FooDB: FOOD00861)

Endogenous

Plant

Coffea (HMDB: HMDB0039832)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0039832)

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	719 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	11.2 g/L	ALOGPS
logP	1.75	ALOGPS
logP	0.71	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Basic)	1.77	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	42.92 m³·mol⁻¹	ChemAxon
Polarizability	17.13 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
DarkChem	[M+H]+	132.682	31661259
DarkChem	[M-H]-	131.52	31661259
DeepCCS	[M+H]+	137.929	30932474
DeepCCS	[M-H]-	134.966	30932474
DeepCCS	[M-2H]-	171.599	30932474
DeepCCS	[M+Na]+	147.02	30932474
AllCCS	[M+H]+	132.1	32859911
AllCCS	[M+H-H2O]+	127.5	32859911
AllCCS	[M+NH4]+	136.3	32859911
AllCCS	[M+Na]+	137.5	32859911
AllCCS	[M-H]-	134.6	32859911
AllCCS	[M+Na-2H]-	135.7	32859911
AllCCS	[M+HCOO]-	137.0	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine	CC1CC2=C(C1)N=C(C)C=N2	1698.4	Standard polar	33892256
6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine	CC1CC2=C(C1)N=C(C)C=N2	1178.0	Standard non polar	33892256
6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine	CC1CC2=C(C1)N=C(C)C=N2	1239.4	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 - 6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine GC-MS (Non-derivatized) - 70eV, Positive	splash10-001j-2900000000-cd36283f622656b64a0b	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 6,7-Dihydro-2,6-dimethyl-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 - 6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine 10V, Positive-QTOF	splash10-0002-0900000000-a416f76eda95c2750f5f	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine 20V, Positive-QTOF	splash10-0002-0900000000-ed71e0208dd552834f19	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine 40V, Positive-QTOF	splash10-0560-9700000000-16919ac1e30bbb5f4aac	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine 10V, Negative-QTOF	splash10-0002-0900000000-c9d292b3c75b51bc26ca	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine 20V, Negative-QTOF	splash10-0002-0900000000-3c8fe0f5e93748264e01	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine 40V, Negative-QTOF	splash10-001i-1900000000-e9ac2c8bb9f8874debea	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine 10V, Positive-QTOF	splash10-0002-0900000000-2ef1a63f0d174650da9c	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine 20V, Positive-QTOF	splash10-0002-1900000000-8b71774597d2d94137fe	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine 40V, Positive-QTOF	splash10-004l-9100000000-bdc36767d45495bb5672	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine 10V, Negative-QTOF	splash10-0002-0900000000-aff21bfca25e06c85423	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine 20V, Negative-QTOF	splash10-0002-0900000000-fa521ff3df86da953f14	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine 40V, Negative-QTOF	splash10-0005-7900000000-b37f6cb43ab8f2bde88b	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

FDB019485

KNApSAcK ID

Not Available

Chemspider ID

32686052

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

12306175

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1630341

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 6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine (HMDB0039832)

MOL for HMDB0039832 (6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine)

3D MOL for HMDB0039832 (6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine)

3D SDF for HMDB0039832 (6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine)

3D-SDF for HMDB0039832 (6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine)

PDB for HMDB0039832 (6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine)

3D PDB for HMDB0039832 (6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine)

SMILES for HMDB0039832 (6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine)

INCHI for HMDB0039832 (6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine)

Structure for HMDB0039832 (6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine)

3D Structure for HMDB0039832 (6,7-Dihydro-2,6-dimethyl-5H-cyclopentapyrazine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra