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Showing metabocard for Methanethiol (HMDB0003227)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 15:12:42 UTC
Update Date2023-02-21 17:16:34 UTC
HMDB IDHMDB0003227
Secondary Accession Numbers
  • HMDB03227
Metabolite Identification
Common NameMethanethiol
DescriptionMethanethiol (also known as methyl mercaptan) is a colorless gas that smells like rotten cabbage. It is a natural substance found in the blood, brain, and other tissues of people and animals. It is released from animal feces. It occurs naturally in certain foods, such as some nuts and cheese. It is also one of the main chemicals responsible for bad breath and flatulence. At very high concentrations methanethiol is highly toxic and affects the central nervous system. The chemical formula for methanethiol is CH3SH; it is classified as a thiol. Methanethiol is also considered to be a weak acid, with a pKa of ~10.4. This acidic property makes it reactive with dissolved metals in aqueous solutions. The environmental chemistry of these interactions in seawater or fresh water environments such as lakes has yet to be fully investigated. -- Wikipedia .
Structure
Data?1676999794
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0003227 (Methanethiol)

878
  Mrv1652309042000282D          

  2  1  0  0  0  0            999 V2000
    2.0926   -0.2063    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.8070    0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
M  END
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3D MOL for HMDB0003227 (Methanethiol)

HMDB0003227
     RDKit          3D
Methanethiol
  6  5  0  0  0  0  0  0  0  0999 V2000
   -0.5142    0.0110   -0.0193 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1645    0.4674   -0.4104 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1775    0.8806   -0.2678 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9092   -0.8384   -0.6186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6924   -0.2256    1.0397 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1289   -0.2950    0.2764 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  1  3  1  0
  1  4  1  0
  1  5  1  0
  2  6  1  0
M  END
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3D SDF for HMDB0003227 (Methanethiol)

878
  Mrv1652309042000282D          

  2  1  0  0  0  0            999 V2000
    2.0926   -0.2063    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.8070    0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0003227

> <DATABASE_NAME>
hmdb

> <SMILES>
CS

> <INCHI_IDENTIFIER>
InChI=1S/CH4S/c1-2/h2H,1H3

> <INCHI_KEY>
LSDPWZHWYPCBBB-UHFFFAOYSA-N

> <FORMULA>
CH4S

> <MOLECULAR_WEIGHT>
48.107

> <EXACT_MASS>
48.003370818

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
5.334205728542365

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methanethiol

> <ALOGPS_LOGP>
0.73

> <JCHEM_LOGP>
0.8365702916666667

> <ALOGPS_LOGS>
-0.38

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.3368127837657

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
14.2407

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.00e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methanethiol

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0003227 (Methanethiol)

HMDB0003227
     RDKit          3D
Methanethiol
  6  5  0  0  0  0  0  0  0  0999 V2000
   -0.5142    0.0110   -0.0193 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1645    0.4674   -0.4104 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1775    0.8806   -0.2678 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9092   -0.8384   -0.6186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6924   -0.2256    1.0397 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1289   -0.2950    0.2764 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  1  3  1  0
  1  4  1  0
  1  5  1  0
  2  6  1  0
M  END
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PDB for HMDB0003227 (Methanethiol)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 878                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  S   UNK     0       3.906  -0.385   0.000  0.00  0.00           S+0
HETATM    2  C   UNK     0       5.240   0.385   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1                                                            
MASTER        0    0    0    0    0    0    0    0    2    0    2    0
END
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3D PDB for HMDB0003227 (Methanethiol)

COMPND    HMDB0003227
HETATM    1  C1  UNL     1      -0.514   0.011  -0.019  1.00  0.00           C  
HETATM    2  S1  UNL     1       1.164   0.467  -0.410  1.00  0.00           S  
HETATM    3  H1  UNL     1      -1.178   0.881  -0.268  1.00  0.00           H  
HETATM    4  H2  UNL     1      -0.909  -0.838  -0.619  1.00  0.00           H  
HETATM    5  H3  UNL     1      -0.692  -0.226   1.040  1.00  0.00           H  
HETATM    6  H4  UNL     1       2.129  -0.295   0.276  1.00  0.00           H  
CONECT    1    2    3    4    5
CONECT    2    6
END
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SMILES for HMDB0003227 (Methanethiol)

CS
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INCHI for HMDB0003227 (Methanethiol)

InChI=1S/CH4S/c1-2/h2H,1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
MethylmercaptanChEBI
CH3SHHMDB
Mercaptan methyliqueHMDB
MercaptomethaneHMDB
MethanethioleHMDB
MethanthiolHMDB
MethvtioloHMDB
Methyl mercaptanHMDB
Methyl sulfhydrateHMDB
Methyl thioalcoholHMDB
MethylmercaptaanHMDB
MetilmercaptanoHMDB
ThiomethaneHMDB
ThiomethanolHMDB
Methylmercaptan, lead (2+) saltMeSH, HMDB
MethanethiolateMeSH, HMDB
Methylmercaptan, sodium saltMeSH, HMDB
Methylmercaptan, mercury (2+) saltMeSH, HMDB
Chemical FormulaCH4S
Average Molecular Weight48.107
Monoisotopic Molecular Weight48.003370818
IUPAC Namemethanethiol
Traditional Namemethanethiol
CAS Registry Number74-93-1
SMILES
CS
InChI Identifier
InChI=1S/CH4S/c1-2/h2H,1H3
InChI KeyLSDPWZHWYPCBBB-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alkylthiols. These are organic compounds containing the thiol functional group linked to an alkyl chain.
KingdomOrganic compounds
Super ClassOrganosulfur compounds
ClassThiols
Sub ClassAlkylthiols
Direct ParentAlkylthiols
Alternative Parents
Substituents
  • Alkylthiol
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Not AvailableNot Available
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-123 °CNot Available
Boiling Point6.10 to 6.20 °C. @ 727.00 mm HgThe Good Scents Company Information System
Water Solubility15.4 mg/mL at 25 °CNot Available
LogP0.932 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility20 g/LALOGPS
logP0.73ALOGPS
logP0.84ChemAxon
logS-0.38ALOGPS
pKa (Strongest Acidic)10.34ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity14.24 m³·mol⁻¹ChemAxon
Polarizability5.33 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+112.18930932474
DeepCCS[M-H]-110.43330932474
DeepCCS[M-2H]-145.64630932474
DeepCCS[M+Na]+118.99930932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
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, 2022.0.2 minutes32390414
Predicted by Siyang on May 30, 202214.2086 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.55 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1663.2 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid634.5 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid249.8 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid496.1 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid321.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid490.7 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid672.8 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)1011.0 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1064.6 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid282.0 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1188.5 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid443.0 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid464.0 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate944.0 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA556.3 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water267.1 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
MethanethiolCS658.2Standard polar33892256
MethanethiolCS418.5Standard non polar33892256
MethanethiolCS397.2Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Methanethiol,1TMS,isomer #1CS[Si](C)(C)C679.2Semi standard non polar33892256
Methanethiol,1TMS,isomer #1CS[Si](C)(C)C723.1Standard non polar33892256
Methanethiol,1TMS,isomer #1CS[Si](C)(C)C772.0Standard polar33892256
Methanethiol,1TBDMS,isomer #1CS[Si](C)(C)C(C)(C)C941.7Semi standard non polar33892256
Methanethiol,1TBDMS,isomer #1CS[Si](C)(C)C(C)(C)C927.3Standard non polar33892256
Methanethiol,1TBDMS,isomer #1CS[Si](C)(C)C(C)(C)C945.1Standard polar33892256
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue Locations
  • Fibroblasts
  • Intestine
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified5.7 +/- 0.3 uMAdult (>18 years old)BothNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Not Specified
Normal		 details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.516 +/- 0.068 uMAdult (>18 years old)BothCirrhosis details
BloodDetected and Quantified1.211 +/- 0.128 uMAdult (>18 years old)Both
Cirrhosis		 details
BloodDetected and Quantified7.7 +/- 1.1 uMAdult (>18 years old)BothLiver disease (non-encephalopathic) details
BloodDetected and Quantified13.2 +/- 1.0 uMAdult (>18 years old)BothLiver disease (encephalopathic) details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Campylobacter jejuni infection		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Clostridium difficile infection		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Ulcerative Colitis		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Nonalcoholic fatty liver disease (NAFLD)		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Ulcerative colitis		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Crohn's disease 		details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothBreast cancer details
Associated Disorders and Diseases
Disease References
Cirrhosis
  1. McClain CJ, Zieve L, Doizaki WM, Gilberstadt S, Onstad GR: Blood methanethiol in alcoholic liver disease with and without hepatic encephalopathy. Gut. 1980 Apr;21(4):318-23. [PubMed:7429293 ]
Liver disease
  1. Fabbri EL, Hamner LH 3rd: Congenital complete heart block associated with maternal anti-Ro antibody: a case report. J Perinatol. 1992 Sep;12(3):225-8. [PubMed:1432277 ]
Ulcerative colitis
  1. Garner CE, Smith S, de Lacy Costello B, White P, Spencer R, Probert CS, Ratcliffe NM: Volatile organic compounds from feces and their potential for diagnosis of gastrointestinal disease. FASEB J. 2007 Jun;21(8):1675-88. Epub 2007 Feb 21. [PubMed:17314143 ]
  2. De Preter V, Machiels K, Joossens M, Arijs I, Matthys C, Vermeire S, Rutgeerts P, Verbeke K: Faecal metabolite profiling identifies medium-chain fatty acids as discriminating compounds in IBD. Gut. 2015 Mar;64(3):447-58. doi: 10.1136/gutjnl-2013-306423. Epub 2014 May 8. [PubMed:24811995 ]
Nonalcoholic fatty liver disease
  1. Raman M, Ahmed I, Gillevet PM, Probert CS, Ratcliffe NM, Smith S, Greenwood R, Sikaroodi M, Lam V, Crotty P, Bailey J, Myers RP, Rioux KP: Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease. Clin Gastroenterol Hepatol. 2013 Jul;11(7):868-75.e1-3. doi: 10.1016/j.cgh.2013.02.015. Epub 2013 Feb 27. [PubMed:23454028 ]
Crohn's disease
  1. De Preter V, Machiels K, Joossens M, Arijs I, Matthys C, Vermeire S, Rutgeerts P, Verbeke K: Faecal metabolite profiling identifies medium-chain fatty acids as discriminating compounds in IBD. Gut. 2015 Mar;64(3):447-58. doi: 10.1136/gutjnl-2013-306423. Epub 2014 May 8. [PubMed:24811995 ]
Perillyl alcohol administration for cancer treatment
  1. Silva CL, Passos M, Camara JS: Solid phase microextraction, mass spectrometry and metabolomic approaches for detection of potential urinary cancer biomarkers--a powerful strategy for breast cancer diagnosis. Talanta. 2012 Jan 30;89:360-8. doi: 10.1016/j.talanta.2011.12.041. Epub 2011 Dec 22. [PubMed:22284503 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB011886
KNApSAcK IDC00001258
Chemspider ID855
KEGG Compound IDC00409
BioCyc IDCPD-7671
BiGG IDNot Available
Wikipedia LinkMethanethiol
METLIN ID3204
PubChem Compound878
PDB IDNot Available
ChEBI ID16007
Food Biomarker OntologyNot Available
VMH IDCH4S
MarkerDB IDMDB00000415
Good Scents IDrw1008781
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Jiang T, Suarez FL, Levitt MD, Nelson SE, Ziegler EE: Gas production by feces of infants. J Pediatr Gastroenterol Nutr. 2001 May;32(5):534-41. [PubMed:11429513 ]
  2. Walker V, Mills GA, Fortune PM, Wheeler R: Neonatal encephalopathy with a pungent body odour. Arch Dis Child Fetal Neonatal Ed. 1997 Jul;77(1):F65-6. [PubMed:9279187 ]
  3. Suarez F, Springfield J, Furne J, Levitt M: Differentiation of mouth versus gut as site of origin of odoriferous breath gases after garlic ingestion. Am J Physiol. 1999 Feb;276(2 Pt 1):G425-30. [PubMed:9950816 ]
  4. Yaegaki K, Sanada K: Volatile sulfur compounds in mouth air from clinically healthy subjects and patients with periodontal disease. J Periodontal Res. 1992 Jul;27(4 Pt 1):233-8. [PubMed:1640345 ]
  5. Suarez FL, Furne J, Springfield J, Levitt MD: Failure of activated charcoal to reduce the release of gases produced by the colonic flora. Am J Gastroenterol. 1999 Jan;94(1):208-12. [PubMed:9934757 ]
  6. Jonski G, Young A, Waler SM, Rolla G: Insoluble zinc, cupric and tin pyrophosphates inhibit the formation of volatile sulphur compounds. Eur J Oral Sci. 2004 Oct;112(5):429-32. [PubMed:15458502 ]
  7. Hayward NJ, Jeavons TH, Nicholson AJ, Thornton AG: Development of specific tests for rapid detection of Escherichia coli and all species of Proteus in urine. J Clin Microbiol. 1977 Sep;6(3):195-201. [PubMed:332706 ]
  8. Johnson PW, Lancero H: Function of gingival fibroblasts and periodontal ligament cells in the presence of methyl mercaptan. Quintessence Int. 1999 May;30(5):343-9. [PubMed:10635290 ]