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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 23:31:05 UTC

Update Date

2021-09-26 22:55:38 UTC

HMDB ID

HMDB0246500

Secondary Accession Numbers

None

Metabolite Identification

Common Name

2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-

Description

7-methyl-1H-1,3-benzodiazole-2-thiol belongs to the class of organic compounds known as benzimidazoles. These are organic compounds containing a benzene ring fused to an imidazole ring (five member ring containing a nitrogen atom, 4 carbon atoms, and two double bonds). 7-methyl-1H-1,3-benzodiazole-2-thiol is a strong basic compound (based on its pKa). This compound has been identified in human blood as reported by (PMID: 31557052 ). 2h-benzimidazole-2-thione, 1,3-dihydro-4-methyl- is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl- 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 Stereo Labels

Synonyms

Value	Source
2-MMBI	MeSH
2-Mercaptomethylbenzimidazole	MeSH
Nocrac MMB	MeSH

Chemical Formula

C₈H₈N₂S

Average Molecular Weight

164.23

Monoisotopic Molecular Weight

164.04081944

IUPAC Name

7-methyl-1H-1,3-benzodiazole-2-thiol

Traditional Name

4-methyl-3H-1,3-benzodiazole-2-thiol

CAS Registry Number

Not Available

SMILES

CC1=C2NC(S)=NC2=CC=C1

InChI Identifier

InChI=1S/C8H8N2S/c1-5-3-2-4-6-7(5)10-8(11)9-6/h2-4H,1H3,(H2,9,10,11)

InChI Key

UDQCDDZBBZNIFA-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzimidazoles. These are organic compounds containing a benzene ring fused to an imidazole ring (five member ring containing a nitrogen atom, 4 carbon atoms, and two double bonds).

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzimidazoles

Sub Class

Not Available

Direct Parent

Benzimidazoles

Alternative Parents

Substituents

Benzimidazole
Benzenoid
Imidazole-2-thione
Heteroaromatic compound
Imidazole
Azole
Thiourea
Azacycle
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Organosulfur compound
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	2.02	ALOGPS
logP	2.55	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	8.32	ChemAxon
pKa (Strongest Basic)	4.99	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	28.68 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	47.49 m³·mol⁻¹	ChemAxon
Polarizability	17.64 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]+	134.977	30932474
DeepCCS	[M-H]-	131.963	30932474
DeepCCS	[M-2H]-	168.793	30932474
DeepCCS	[M+Na]+	144.332	30932474
AllCCS	[M+H]+	130.5	32859911
AllCCS	[M+H-H2O]+	125.8	32859911
AllCCS	[M+NH4]+	134.8	32859911
AllCCS	[M+Na]+	136.0	32859911
AllCCS	[M-H]-	127.5	32859911
AllCCS	[M+Na-2H]-	128.3	32859911
AllCCS	[M+HCOO]-	129.2	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-	CC1=C2NC(S)=NC2=CC=C1	2698.6	Standard polar	33892256
2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-	CC1=C2NC(S)=NC2=CC=C1	1952.2	Standard non polar	33892256
2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-	CC1=C2NC(S)=NC2=CC=C1	2278.5	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-,1TMS,isomer #1	CC1=CC=CC2=C1[NH]C(S[Si](C)(C)C)=N2	1808.2	Semi standard non polar	33892256
2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-,1TMS,isomer #1	CC1=CC=CC2=C1[NH]C(S[Si](C)(C)C)=N2	1791.6	Standard non polar	33892256
2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-,1TMS,isomer #1	CC1=CC=CC2=C1[NH]C(S[Si](C)(C)C)=N2	2328.5	Standard polar	33892256
2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-,1TMS,isomer #2	CC1=CC=CC2=C1N([Si](C)(C)C)C(S)=N2	1898.2	Semi standard non polar	33892256
2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-,1TMS,isomer #2	CC1=CC=CC2=C1N([Si](C)(C)C)C(S)=N2	1731.0	Standard non polar	33892256
2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-,1TMS,isomer #2	CC1=CC=CC2=C1N([Si](C)(C)C)C(S)=N2	2104.8	Standard polar	33892256
2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-,2TMS,isomer #1	CC1=CC=CC2=C1N([Si](C)(C)C)C(S[Si](C)(C)C)=N2	2010.2	Semi standard non polar	33892256
2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-,2TMS,isomer #1	CC1=CC=CC2=C1N([Si](C)(C)C)C(S[Si](C)(C)C)=N2	1844.0	Standard non polar	33892256
2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-,2TMS,isomer #1	CC1=CC=CC2=C1N([Si](C)(C)C)C(S[Si](C)(C)C)=N2	2029.8	Standard polar	33892256
2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-,1TBDMS,isomer #1	CC1=CC=CC2=C1[NH]C(S[Si](C)(C)C(C)(C)C)=N2	2052.4	Semi standard non polar	33892256
2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-,1TBDMS,isomer #1	CC1=CC=CC2=C1[NH]C(S[Si](C)(C)C(C)(C)C)=N2	1993.7	Standard non polar	33892256
2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-,1TBDMS,isomer #1	CC1=CC=CC2=C1[NH]C(S[Si](C)(C)C(C)(C)C)=N2	2424.5	Standard polar	33892256
2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-,1TBDMS,isomer #2	CC1=CC=CC2=C1N([Si](C)(C)C(C)(C)C)C(S)=N2	2135.5	Semi standard non polar	33892256
2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-,1TBDMS,isomer #2	CC1=CC=CC2=C1N([Si](C)(C)C(C)(C)C)C(S)=N2	1936.3	Standard non polar	33892256
2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-,1TBDMS,isomer #2	CC1=CC=CC2=C1N([Si](C)(C)C(C)(C)C)C(S)=N2	2208.6	Standard polar	33892256
2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-,2TBDMS,isomer #1	CC1=CC=CC2=C1N([Si](C)(C)C(C)(C)C)C(S[Si](C)(C)C(C)(C)C)=N2	2364.7	Semi standard non polar	33892256
2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-,2TBDMS,isomer #1	CC1=CC=CC2=C1N([Si](C)(C)C(C)(C)C)C(S[Si](C)(C)C(C)(C)C)=N2	2279.3	Standard non polar	33892256
2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-,2TBDMS,isomer #1	CC1=CC=CC2=C1N([Si](C)(C)C(C)(C)C)C(S[Si](C)(C)C(C)(C)C)=N2	2279.7	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl- GC-MS (Non-derivatized) - 70eV, Positive	splash10-08fr-0900000000-a6551ec0a82374c7209f	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl- 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 - 2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl- 10V, Positive-QTOF	splash10-014i-0900000000-9d9787ac0e629074480a	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl- 20V, Positive-QTOF	splash10-014i-0900000000-e3b73f493467daad1067	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl- 40V, Positive-QTOF	splash10-0kdl-9800000000-3b5a8a6feffc21531087	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl- 10V, Negative-QTOF	splash10-03di-0900000000-2bc8964eff5dcc3e751c	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl- 20V, Negative-QTOF	splash10-03xr-0900000000-5a11868cfd52bfc8531e	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl- 40V, Negative-QTOF	splash10-0560-9600000000-3ca8e0ea7236525633e4	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl- 10V, Positive-QTOF	splash10-014i-0900000000-8a1b6860245adc5f41d6	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl- 20V, Positive-QTOF	splash10-014i-0900000000-2fcdafce8ce931e80484	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl- 40V, Positive-QTOF	splash10-0fc0-6900000000-dbbf4ee3575750a442fc	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl- 10V, Negative-QTOF	splash10-004i-0900000000-92ad1adb0c25799beef6	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl- 20V, Negative-QTOF	splash10-01t9-0900000000-5ef5920bd759df3e48b7	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl- 40V, Negative-QTOF	splash10-0ar0-5900000000-64f948d3e90b9be7f101	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

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

97521

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 2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl- (HMDB0246500)

MOL for HMDB0246500 (2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-)

3D MOL for HMDB0246500 (2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-)

3D SDF for HMDB0246500 (2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-)

3D-SDF for HMDB0246500 (2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-)

PDB for HMDB0246500 (2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-)

3D PDB for HMDB0246500 (2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-)

SMILES for HMDB0246500 (2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-)

INCHI for HMDB0246500 (2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-)

Structure for HMDB0246500 (2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-)

3D Structure for HMDB0246500 (2H-Benzimidazole-2-thione, 1,3-dihydro-4-methyl-)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra