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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 01:20:02 UTC

Update Date

2023-02-21 17:27:10 UTC

HMDB ID

HMDB0039796

Secondary Accession Numbers

HMDB39796

Metabolite Identification

Common Name

4,5-Dihydro-5-methyl-3-thiophenethiol

Description

4,5-Dihydro-5-methyl-3-thiophenethiol belongs to the class of organic compounds known as dihydrothiophenes. Dihydrothiophenes are compounds containing a dihydrothiophene moiety, which is a thiophene derivative with only one double bond. Based on a literature review very few articles have been published on 4,5-Dihydro-5-methyl-3-thiophenethiol.

Structure

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

View in JSmol View Stereo Labels

Synonyms

Value	Source
4-mercapto-2-Methyl-2,3-dihydrothiophene	HMDB

Chemical Formula

C₅H₈S₂

Average Molecular Weight

132.247

Monoisotopic Molecular Weight

132.006741636

IUPAC Name

5-methyl-4,5-dihydrothiophene-3-thiol

Traditional Name

5-methyl-4,5-dihydrothiophene-3-thiol

CAS Registry Number

26486-15-7

SMILES

CC1CC(S)=CS1

InChI Identifier

InChI=1S/C5H8S2/c1-4-2-5(6)3-7-4/h3-4,6H,2H2,1H3

InChI Key

JPJBGDKFMKAFRU-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dihydrothiophenes. Dihydrothiophenes are compounds containing a dihydrothiophene moiety, which is a thiophene derivative with only one double bond.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Dihydrothiophenes

Sub Class

Not Available

Direct Parent

Dihydrothiophenes

Alternative Parents

Substituents

2,3-dihydrothiophene
Thioenolether
Thioenol
Alkylthiol
Hydrocarbon derivative
Organosulfur compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0039796)
Cytoplasm (HMDB: HMDB0039796)

Source

Exogenous

Exogenous (HMDB: HMDB0039796)

Food

Food (HMDB: HMDB0039796)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0039796)

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	986.2 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	1.33 g/L	ALOGPS
logP	2.02	ALOGPS
logP	1.08	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	8.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	0 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	39.41 m³·mol⁻¹	ChemAxon
Polarizability	14.19 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
DeepCCS	[M+H]+	129.587	30932474
DeepCCS	[M-H]-	127.676	30932474
DeepCCS	[M-2H]-	163.581	30932474
DeepCCS	[M+Na]+	138.128	30932474
AllCCS	[M+H]+	124.7	32859911
AllCCS	[M+H-H2O]+	120.0	32859911
AllCCS	[M+NH4]+	129.1	32859911
AllCCS	[M+Na]+	130.4	32859911
AllCCS	[M-H]-	132.0	32859911
AllCCS	[M+Na-2H]-	135.2	32859911
AllCCS	[M+HCOO]-	138.7	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.	3.02 minutes	32390414
Predicted by Siyang on May 30, 2022	14.7971 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.12 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1948.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	580.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	227.1 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	413.0 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	206.7 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	538.6 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	653.5 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	562.5 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1128.6 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	410.2 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	1275.7 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	428.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	419.0 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	755.0 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	624.7 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	199.6 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
4,5-Dihydro-5-methyl-3-thiophenethiol	CC1CC(S)=CS1	1613.6	Standard polar	33892256
4,5-Dihydro-5-methyl-3-thiophenethiol	CC1CC(S)=CS1	1030.4	Standard non polar	33892256
4,5-Dihydro-5-methyl-3-thiophenethiol	CC1CC(S)=CS1	1136.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
4,5-Dihydro-5-methyl-3-thiophenethiol,1TMS,isomer #1	CC1CC(S[Si](C)(C)C)=CS1	1364.6	Semi standard non polar	33892256
4,5-Dihydro-5-methyl-3-thiophenethiol,1TMS,isomer #1	CC1CC(S[Si](C)(C)C)=CS1	1180.2	Standard non polar	33892256
4,5-Dihydro-5-methyl-3-thiophenethiol,1TBDMS,isomer #1	CC1CC(S[Si](C)(C)C(C)(C)C)=CS1	1611.7	Semi standard non polar	33892256
4,5-Dihydro-5-methyl-3-thiophenethiol,1TBDMS,isomer #1	CC1CC(S[Si](C)(C)C(C)(C)C)=CS1	1431.8	Standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 4,5-Dihydro-5-methyl-3-thiophenethiol GC-MS (Non-derivatized) - 70eV, Positive	splash10-007n-9100000000-fb761ed443d98c20c2bd	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4,5-Dihydro-5-methyl-3-thiophenethiol 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 - 4,5-Dihydro-5-methyl-3-thiophenethiol 10V, Positive-QTOF	splash10-001i-4900000000-26af50ae65e1833bdf02	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4,5-Dihydro-5-methyl-3-thiophenethiol 20V, Positive-QTOF	splash10-001i-8900000000-a84538db84c7991d3198	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4,5-Dihydro-5-methyl-3-thiophenethiol 40V, Positive-QTOF	splash10-0udi-9000000000-db146bdc6650a89b0bcf	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4,5-Dihydro-5-methyl-3-thiophenethiol 10V, Negative-QTOF	splash10-001i-4900000000-09bf7a81e2d4a3049195	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4,5-Dihydro-5-methyl-3-thiophenethiol 20V, Negative-QTOF	splash10-053i-9200000000-8f83a7707c1d1f116c60	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4,5-Dihydro-5-methyl-3-thiophenethiol 40V, Negative-QTOF	splash10-000i-9000000000-6f408cfaaffa07809bcb	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4,5-Dihydro-5-methyl-3-thiophenethiol 10V, Negative-QTOF	splash10-001i-3900000000-0d28d71ecac14dce284e	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4,5-Dihydro-5-methyl-3-thiophenethiol 20V, Negative-QTOF	splash10-000t-9700000000-7d4bdc33c27e64362e07	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4,5-Dihydro-5-methyl-3-thiophenethiol 40V, Negative-QTOF	splash10-001i-7900000000-d38665296cd9cab2ee30	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4,5-Dihydro-5-methyl-3-thiophenethiol 10V, Positive-QTOF	splash10-001i-3900000000-978866cf09e85602d436	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4,5-Dihydro-5-methyl-3-thiophenethiol 20V, Positive-QTOF	splash10-0a4m-9000000000-bdf9f28bfeeaa17b66bf	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4,5-Dihydro-5-methyl-3-thiophenethiol 40V, Positive-QTOF	splash10-05mk-9000000000-8b4edf31e25e08f3a5e3	2021-09-23	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+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

FDB019446

KNApSAcK ID

Not Available

Chemspider ID

15411781

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

20362520

PDB ID

Not Available

ChEBI ID

173529

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1880351

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 4,5-Dihydro-5-methyl-3-thiophenethiol (HMDB0039796)

MOL for HMDB0039796 (4,5-Dihydro-5-methyl-3-thiophenethiol)

3D MOL for HMDB0039796 (4,5-Dihydro-5-methyl-3-thiophenethiol)

3D SDF for HMDB0039796 (4,5-Dihydro-5-methyl-3-thiophenethiol)

3D-SDF for HMDB0039796 (4,5-Dihydro-5-methyl-3-thiophenethiol)

PDB for HMDB0039796 (4,5-Dihydro-5-methyl-3-thiophenethiol)

3D PDB for HMDB0039796 (4,5-Dihydro-5-methyl-3-thiophenethiol)

SMILES for HMDB0039796 (4,5-Dihydro-5-methyl-3-thiophenethiol)

INCHI for HMDB0039796 (4,5-Dihydro-5-methyl-3-thiophenethiol)

Structure for HMDB0039796 (4,5-Dihydro-5-methyl-3-thiophenethiol)

3D Structure for HMDB0039796 (4,5-Dihydro-5-methyl-3-thiophenethiol)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

IR Spectra