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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 01:36:17 UTC

Update Date

2023-02-21 17:27:33 UTC

HMDB ID

HMDB0040060

Secondary Accession Numbers

HMDB40060

Metabolite Identification

Common Name

2-Methyl-5-(methylthio)pyrazine

Description

2-Methyl-5-(methylthio)pyrazine belongs to the class of organic compounds known as aryl thioethers. These are organosulfur compounds containing a thioether group that is substituted by an aryl group. Based on a literature review very few articles have been published on 2-Methyl-5-(methylthio)pyrazine.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
2-Methyl-6-(methylsulfanyl)pyrazine	HMDB
2-methylthio-6-Methylpyrazine	HMDB
CTOP	HMDB
Ctop-NH2	HMDB
Ctopa	HMDB
Cys(2)-tyr(3)-orn(5)-pen(7)-amide	HMDB
Phe-cycl(cys-tyr-TRP-orn-THR-pen)THR-NH2	HMDB
2-Methyl-5-(methylsulphanyl)pyrazine	Generator

Chemical Formula

C₆H₈N₂S

Average Molecular Weight

140.206

Monoisotopic Molecular Weight

140.040818956

IUPAC Name

2-methyl-5-(methylsulfanyl)pyrazine

Traditional Name

2-methyl-5-(methylsulfanyl)pyrazine

CAS Registry Number

2884-13-1

SMILES

CSC1=NC=C(C)N=C1

InChI Identifier

InChI=1S/C6H8N2S/c1-5-3-8-6(9-2)4-7-5/h3-4H,1-2H3

InChI Key

DNBQBSWEJGAAIY-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aryl thioethers. These are organosulfur compounds containing a thioether group that is substituted by an aryl group.

Kingdom

Organic compounds

Super Class

Organosulfur compounds

Class

Thioethers

Sub Class

Aryl thioethers

Direct Parent

Aryl thioethers

Alternative Parents

Substituents

Aryl thioether
Alkylarylthioether
Pyrazine
Heteroaromatic compound
Azacycle
Organoheterocyclic compound
Sulfenyl compound
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0040060)
Cytoplasm (HMDB: HMDB0040060)

Source

Exogenous

Exogenous (HMDB: HMDB0040060)

Food

Food (HMDB: HMDB0040060)

Process

Not Available

Role

Industrial application

Food and nutrition

Food additive

Flavoring agent

Flavoring Agent (HMDB: HMDB0040060)

Biological role

Nutrient (HMDB: HMDB0040060)

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
Water Solubility	18.6 g/L	ALOGPS
logP	1.55	ALOGPS
logP	0.89	ChemAxon
logS	-0.88	ALOGPS
pKa (Strongest Basic)	0.82	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	1	ChemAxon
Refractivity	39.41 m³·mol⁻¹	ChemAxon
Polarizability	14.89 Å³	ChemAxon
Number of Rings	1	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]+	128.724	31661259
DarkChem	[M-H]-	126.602	31661259
DeepCCS	[M+H]+	130.139	30932474
DeepCCS	[M-H]-	126.497	30932474
DeepCCS	[M-2H]-	163.803	30932474
DeepCCS	[M+Na]+	139.018	30932474
AllCCS	[M+H]+	128.3	32859911
AllCCS	[M+H-H2O]+	123.7	32859911
AllCCS	[M+NH4]+	132.6	32859911
AllCCS	[M+Na]+	133.8	32859911
AllCCS	[M-H]-	130.4	32859911
AllCCS	[M+Na-2H]-	132.6	32859911
AllCCS	[M+HCOO]-	135.0	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.	2.7 minutes	32390414
Predicted by Siyang on May 30, 2022	12.3727 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.1 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	45.5 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1217.9 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	459.8 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	164.8 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	303.4 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	151.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	421.5 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	412.1 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	121.3 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	993.6 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	107.8 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	973.6 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	336.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	320.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	535.1 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	515.8 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	112.0 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2-Methyl-5-(methylthio)pyrazine	CSC1=NC=C(C)N=C1	1625.4	Standard polar	33892256
2-Methyl-5-(methylthio)pyrazine	CSC1=NC=C(C)N=C1	1162.6	Standard non polar	33892256
2-Methyl-5-(methylthio)pyrazine	CSC1=NC=C(C)N=C1	1211.9	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 - 2-Methyl-5-(methylthio)pyrazine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0f6x-9600000000-bfcd45f47dce41df41b4	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Methyl-5-(methylthio)pyrazine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Methyl-5-(methylthio)pyrazine 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 - 2-Methyl-5-(methylthio)pyrazine 10V, Positive-QTOF	splash10-0006-0900000000-2f672bd4df3f820965b5	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-5-(methylthio)pyrazine 20V, Positive-QTOF	splash10-0006-1900000000-e92a672b114137585df3	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-5-(methylthio)pyrazine 40V, Positive-QTOF	splash10-0006-9200000000-ef6a4ef6fc593b65de73	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-5-(methylthio)pyrazine 10V, Negative-QTOF	splash10-000i-1900000000-aecf5e42180239ac6b6e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-5-(methylthio)pyrazine 20V, Negative-QTOF	splash10-000l-6900000000-78ffc9b10743ceb0fc1d	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-5-(methylthio)pyrazine 40V, Negative-QTOF	splash10-0006-9000000000-6c9fb9636f19db629de3	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-5-(methylthio)pyrazine 10V, Positive-QTOF	splash10-0006-1900000000-3afa844228bb8c4bcd9d	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-5-(methylthio)pyrazine 20V, Positive-QTOF	splash10-0006-9400000000-d559f1b40966f771ffd0	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-5-(methylthio)pyrazine 40V, Positive-QTOF	splash10-0uxu-9000000000-56c78f678907f23f1daf	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-5-(methylthio)pyrazine 10V, Negative-QTOF	splash10-000i-0900000000-8754f1c7eda7838acfde	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-5-(methylthio)pyrazine 20V, Negative-QTOF	splash10-00ko-9300000000-983149fae86dafffff82	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Methyl-5-(methylthio)pyrazine 40V, Negative-QTOF	splash10-0006-9000000000-7cc3e76a04cc8a1f70d1	2021-09-24	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
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, 1000 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, 200 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, 300 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, 400 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, 500 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, 600 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, 700 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, 800 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, 900 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

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

FDB019747

KNApSAcK ID

Not Available

Chemspider ID

460292

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

528143

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

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for 2-Methyl-5-(methylthio)pyrazine (HMDB0040060)

MOL for HMDB0040060 (2-Methyl-5-(methylthio)pyrazine)

3D MOL for HMDB0040060 (2-Methyl-5-(methylthio)pyrazine)

3D SDF for HMDB0040060 (2-Methyl-5-(methylthio)pyrazine)

3D-SDF for HMDB0040060 (2-Methyl-5-(methylthio)pyrazine)

PDB for HMDB0040060 (2-Methyl-5-(methylthio)pyrazine)

3D PDB for HMDB0040060 (2-Methyl-5-(methylthio)pyrazine)

SMILES for HMDB0040060 (2-Methyl-5-(methylthio)pyrazine)

INCHI for HMDB0040060 (2-Methyl-5-(methylthio)pyrazine)

Structure for HMDB0040060 (2-Methyl-5-(methylthio)pyrazine)

3D Structure for HMDB0040060 (2-Methyl-5-(methylthio)pyrazine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra