Hmdb loader

Showing metabocard for Methanedithiol (HMDB0040184)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 01:43:34 UTC
Update Date2023-02-21 17:27:50 UTC
HMDB IDHMDB0040184
Secondary Accession Numbers
  • HMDB40184
Metabolite Identification
Common NameMethanedithiol
DescriptionMethanedithiol belongs to the class of organic compounds known as alkylthiols. These are organic compounds containing the thiol functional group linked to an alkyl chain. Methanedithiol is a pungent tasting compound. Methanedithiol has been detected, but not quantified in, several different foods, such as oyster mushrooms (Pleurotus ostreatus), garden onion (var.), common mushrooms (Agaricus bisporus), green onion, and garden onions (Allium cepa). This could make methanedithiol a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on Methanedithiol.
Structure
Data?1677000470
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0040184 (Methanedithiol)


  Mrv0541 05061311412D          

  3  2  0  0  0  0            999 V2000
    1.9520   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.7145    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
M  END
Download

3D MOL for HMDB0040184 (Methanedithiol)

HMDB0040184
     RDKit          3D
Methanedithiol
  7  6  0  0  0  0  0  0  0  0999 V2000
    1.0955   -1.0606   -0.2570 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5756   -0.4741    0.0123 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7605    1.2989   -0.2858 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.0800   -0.1269    0.0697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9553   -0.6695    1.0462 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2478   -1.0012   -0.7110 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3638    2.0333    0.1256 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  1  4  1  0
  2  5  1  0
  2  6  1  0
  3  7  1  0
M  END
Download

3D SDF for HMDB0040184 (Methanedithiol)


  Mrv0541 05061311412D          

  3  2  0  0  0  0            999 V2000
    1.9520   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.7145    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0040184

> <DATABASE_NAME>
hmdb

> <SMILES>
SCS

> <INCHI_IDENTIFIER>
InChI=1S/CH4S2/c2-1-3/h2-3H,1H2

> <INCHI_KEY>
INBDPOJZYZJUDA-UHFFFAOYSA-N

> <FORMULA>
CH4S2

> <MOLECULAR_WEIGHT>
80.172

> <EXACT_MASS>
79.975441508

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
8.239450551370933

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methanedithiol

> <ALOGPS_LOGP>
0.55

> <JCHEM_LOGP>
1.043194799

> <ALOGPS_LOGS>
-1.30

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.297074479627867

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.417361191627219

> <JCHEM_PKA_STRONGEST_BASIC>
-9.919321745143613

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
21.7055

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.06e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methanedithiol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0040184 (Methanedithiol)

HMDB0040184
     RDKit          3D
Methanedithiol
  7  6  0  0  0  0  0  0  0  0999 V2000
    1.0955   -1.0606   -0.2570 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5756   -0.4741    0.0123 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7605    1.2989   -0.2858 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.0800   -0.1269    0.0697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9553   -0.6695    1.0462 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2478   -1.0012   -0.7110 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3638    2.0333    0.1256 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  1  4  1  0
  2  5  1  0
  2  6  1  0
  3  7  1  0
M  END
Download

PDB for HMDB0040184 (Methanedithiol)

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       3.644  -2.104   0.000  0.00  0.00           C+0
HETATM    2  S   UNK     0       2.310  -1.334   0.000  0.00  0.00           S+0
HETATM    3  S   UNK     0       4.977  -1.334   0.000  0.00  0.00           S+0
CONECT    1    2    3                                                       
CONECT    2    1                                                            
CONECT    3    1                                                            
MASTER        0    0    0    0    0    0    0    0    3    0    4    0
END
Download

3D PDB for HMDB0040184 (Methanedithiol)

COMPND    HMDB0040184
HETATM    1  S1  UNL     1       1.096  -1.061  -0.257  1.00  0.00           S  
HETATM    2  C1  UNL     1      -0.576  -0.474   0.012  1.00  0.00           C  
HETATM    3  S2  UNL     1      -0.761   1.299  -0.286  1.00  0.00           S  
HETATM    4  H1  UNL     1       2.080  -0.127   0.070  1.00  0.00           H  
HETATM    5  H2  UNL     1      -0.955  -0.670   1.046  1.00  0.00           H  
HETATM    6  H3  UNL     1      -1.248  -1.001  -0.711  1.00  0.00           H  
HETATM    7  H4  UNL     1       0.364   2.033   0.126  1.00  0.00           H  
CONECT    1    2    4
CONECT    2    3    5    6
CONECT    3    7
END
Download

SMILES for HMDB0040184 (Methanedithiol)

SCS
Download

INCHI for HMDB0040184 (Methanedithiol)

InChI=1S/CH4S2/c2-1-3/h2-3H,1H2
Download
View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
DimercaptomethaneHMDB
DithiomethaneHMDB
Chemical FormulaCH4S2
Average Molecular Weight80.172
Monoisotopic Molecular Weight79.975441508
IUPAC Namemethanedithiol
Traditional Namemethanedithiol
CAS Registry Number6725-64-0
SMILES
SCS
InChI Identifier
InChI=1S/CH4S2/c2-1-3/h2-3H,1H2
InChI KeyINBDPOJZYZJUDA-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 DescriptorsNot Available
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point118.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility31740 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP1.386 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility4.06 g/LALOGPS
logP0.55ALOGPS
logP1.04ChemAxon
logS-1.3ALOGPS
pKa (Strongest Acidic)9.42ChemAxon
pKa (Strongest Basic)-9.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity21.71 m³·mol⁻¹ChemAxon
Polarizability8.24 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
DarkChem[M+H]+112.64531661259
DarkChem[M-H]-106.00531661259
DeepCCS[M+H]+115.87130932474
DeepCCS[M-H]-114.1230932474
DeepCCS[M-2H]-149.37830932474
DeepCCS[M+Na]+122.78130932474
AllCCS[M+H]+126.032859911
AllCCS[M+H-H2O]+121.732859911
AllCCS[M+NH4]+130.032859911
AllCCS[M+Na]+131.132859911
AllCCS[M-H]-182.232859911
AllCCS[M+Na-2H]-190.732859911
AllCCS[M+HCOO]-199.932859911

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, 2022.1.04 minutes32390414
Predicted by Siyang on May 30, 202211.619 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.28 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid248.1 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1575.2 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid606.1 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid244.9 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid463.7 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid285.8 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid490.4 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 Acid600.1 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)978.1 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1020.6 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid401.6 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1146.4 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid422.7 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid458.8 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate839.6 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA521.0 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water242.1 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
MethanedithiolSCS1192.5Standard polar33892256
MethanedithiolSCS637.7Standard non polar33892256
MethanedithiolSCS716.0Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Methanedithiol,1TMS,isomer #1C[Si](C)(C)SCS1026.1Semi standard non polar33892256
Methanedithiol,1TMS,isomer #1C[Si](C)(C)SCS913.6Standard non polar33892256
Methanedithiol,2TMS,isomer #1C[Si](C)(C)SCS[Si](C)(C)C1201.9Semi standard non polar33892256
Methanedithiol,2TMS,isomer #1C[Si](C)(C)SCS[Si](C)(C)C1141.4Standard non polar33892256
Methanedithiol,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)SCS1227.7Semi standard non polar33892256
Methanedithiol,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)SCS1183.5Standard non polar33892256
Methanedithiol,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)SCS[Si](C)(C)C(C)(C)C1678.4Semi standard non polar33892256
Methanedithiol,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)SCS[Si](C)(C)C(C)(C)C1608.3Standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB019896
KNApSAcK IDNot Available
Chemspider ID122421
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkMethanedithiol
METLIN IDNot Available
PubChem Compound138818
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1590331
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .