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Showing metabocard for 2-Methyl-1,3-dithiolane (HMDB0036179)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 21:14:24 UTC
Update Date2023-02-21 17:25:10 UTC
HMDB IDHMDB0036179
Secondary Accession Numbers
  • HMDB36179
Metabolite Identification
Common Name2-Methyl-1,3-dithiolane
Description2-Methyl-1,3-dithiolane belongs to the class of organic compounds known as 1,3-dithiolanes. These are organic compounds containing a 1,3-dithiolane ring. 1,3-dithiolane moiety is a 5-membered saturated aliphatic ring with three carbon atoms, and two sulfur atoms at the 1- and 3- ring positions. 2-Methyl-1,3-dithiolane is an alliaceous, savory, and smoky tasting compound. Based on a literature review very few articles have been published on 2-Methyl-1,3-dithiolane.
Structure
Data?1677000310
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0036179 (2-Methyl-1,3-dithiolane)


  Mrv1652305261923542D          

  6  6  0  0  0  0            999 V2000
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  4  1  0  0  0  0
  6  3  1  0  0  0  0
  6  4  1  0  0  0  0
M  END
Download

3D MOL for HMDB0036179 (2-Methyl-1,3-dithiolane)

HMDB0036179
     RDKit          3D
2-Methyl-1,3-dithiolane
 14 14  0  0  0  0  0  0  0  0999 V2000
    2.1655    0.1517    0.0643 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9123   -0.2534   -0.6614 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2205    1.1358   -0.9008 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5228    0.7728    0.3248 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7715   -0.6984    0.0728 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0976   -1.3889    0.3523 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.9342    0.6533    1.0273 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7061   -0.7836    0.3318 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7508    0.7910   -0.6058 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1709   -0.7702   -1.5848 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3988    1.3899    0.0965 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1103    0.9410    1.3403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0024   -0.8003   -1.0056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5159   -1.1406    0.7362 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  2  1  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
M  END
Download

3D SDF for HMDB0036179 (2-Methyl-1,3-dithiolane)


  Mrv1652305261923542D          

  6  6  0  0  0  0            999 V2000
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  4  1  0  0  0  0
  6  3  1  0  0  0  0
  6  4  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0036179

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1SCCS1

> <INCHI_IDENTIFIER>
InChI=1S/C4H8S2/c1-4-5-2-3-6-4/h4H,2-3H2,1H3

> <INCHI_KEY>
CARJCVDELAMAEJ-UHFFFAOYSA-N

> <FORMULA>
C4H8S2

> <MOLECULAR_WEIGHT>
120.236

> <EXACT_MASS>
120.006741636

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
12.778105580198318

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-methyl-1,3-dithiolane

> <ALOGPS_LOGP>
1.47

> <JCHEM_LOGP>
1.3287773093333335

> <ALOGPS_LOGS>
-2.09

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
34.243

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.68e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,3-dithiolane, 2-methyl-

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0036179 (2-Methyl-1,3-dithiolane)

HMDB0036179
     RDKit          3D
2-Methyl-1,3-dithiolane
 14 14  0  0  0  0  0  0  0  0999 V2000
    2.1655    0.1517    0.0643 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9123   -0.2534   -0.6614 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2205    1.1358   -0.9008 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5228    0.7728    0.3248 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7715   -0.6984    0.0728 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0976   -1.3889    0.3523 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.9342    0.6533    1.0273 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7061   -0.7836    0.3318 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7508    0.7910   -0.6058 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1709   -0.7702   -1.5848 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3988    1.3899    0.0965 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1103    0.9410    1.3403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0024   -0.8003   -1.0056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5159   -1.1406    0.7362 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  2  1  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
M  END
Download

PDB for HMDB0036179 (2-Methyl-1,3-dithiolane)

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    5  S   UNK     0      -0.186   1.175   0.000  0.00  0.00           S+0
HETATM    6  S   UNK     0       2.306   1.175   0.000  0.00  0.00           S+0
CONECT    1    4                                                            
CONECT    2    3    5                                                       
CONECT    3    2    6                                                       
CONECT    4    1    5    6                                                  
CONECT    5    2    4                                                       
CONECT    6    3    4                                                       
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
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3D PDB for HMDB0036179 (2-Methyl-1,3-dithiolane)

COMPND    HMDB0036179
HETATM    1  C1  UNL     1       2.166   0.152   0.064  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.912  -0.253  -0.661  1.00  0.00           C  
HETATM    3  S1  UNL     1      -0.221   1.136  -0.901  1.00  0.00           S  
HETATM    4  C3  UNL     1      -1.523   0.773   0.325  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.771  -0.698   0.073  1.00  0.00           C  
HETATM    6  S2  UNL     1      -0.098  -1.389   0.352  1.00  0.00           S  
HETATM    7  H1  UNL     1       1.934   0.653   1.027  1.00  0.00           H  
HETATM    8  H2  UNL     1       2.706  -0.784   0.332  1.00  0.00           H  
HETATM    9  H3  UNL     1       2.751   0.791  -0.606  1.00  0.00           H  
HETATM   10  H4  UNL     1       1.171  -0.770  -1.585  1.00  0.00           H  
HETATM   11  H5  UNL     1      -2.399   1.390   0.096  1.00  0.00           H  
HETATM   12  H6  UNL     1      -1.110   0.941   1.340  1.00  0.00           H  
HETATM   13  H7  UNL     1      -2.002  -0.800  -1.006  1.00  0.00           H  
HETATM   14  H8  UNL     1      -2.516  -1.141   0.736  1.00  0.00           H  
CONECT    1    2    7    8    9
CONECT    2    3    6   10
CONECT    3    4
CONECT    4    5   11   12
CONECT    5    6   13   14
END
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SMILES for HMDB0036179 (2-Methyl-1,3-dithiolane)

CC1SCCS1
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INCHI for HMDB0036179 (2-Methyl-1,3-dithiolane)

InChI=1S/C4H8S2/c1-4-5-2-3-6-4/h4H,2-3H2,1H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2-Methyl-1,3-dithiacyclopentaneHMDB
Acetaldehdye ethylene thioacetalHMDB
FEMA 3705HMDB
Chemical FormulaC4H8S2
Average Molecular Weight120.236
Monoisotopic Molecular Weight120.006741636
IUPAC Name2-methyl-1,3-dithiolane
Traditional Name1,3-dithiolane, 2-methyl-
CAS Registry Number5616-51-3
SMILES
CC1SCCS1
InChI Identifier
InChI=1S/C4H8S2/c1-4-5-2-3-6-4/h4H,2-3H2,1H3
InChI KeyCARJCVDELAMAEJ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 1,3-dithiolanes. These are organic compounds containing a 1,3-dithiolane ring. 1,3-Dithiolane moiety is a 5-membered saturated aliphatic ring with three carbon atoms, and two sulfur atoms at the 1- and 3- ring positions.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDithiolanes
Sub Class1,3-dithiolanes
Direct Parent1,3-dithiolanes
Alternative Parents
Substituents
  • 1,3-dithiolane
  • Thioacetal
  • Dialkylthioether
  • Thioether
  • Hydrocarbon derivative
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Industrial applicationBiological role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point65.00 °C. @ 10.00 mm HgThe Good Scents Company Information System
Water Solubility1600 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP1.090 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.97 g/LALOGPS
logP1.47ALOGPS
logP1.33ChemAxon
logS-2.1ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity34.24 m³·mol⁻¹ChemAxon
Polarizability12.78 ųChemAxon
Number of Rings1ChemAxon
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]+122.77931661259
DarkChem[M-H]-116.66331661259
DeepCCS[M+H]+126.6730932474
DeepCCS[M-H]-124.77530932474
DeepCCS[M-2H]-160.20930932474
DeepCCS[M+Na]+134.60330932474
AllCCS[M+H]+119.332859911
AllCCS[M+H-H2O]+114.632859911
AllCCS[M+NH4]+123.732859911
AllCCS[M+Na]+125.032859911
AllCCS[M-H]-129.032859911
AllCCS[M+Na-2H]-132.832859911
AllCCS[M+HCOO]-137.132859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-Methyl-1,3-dithiolaneCC1SCCS11494.6Standard polar33892256
2-Methyl-1,3-dithiolaneCC1SCCS1978.0Standard non polar33892256
2-Methyl-1,3-dithiolaneCC1SCCS11021.5Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 2-Methyl-1,3-dithiolane GC-MS (Non-derivatized) - 70eV, Positivesplash10-05i3-9300000000-81c86a79c45d84fe5ac42017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Methyl-1,3-dithiolane GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methyl-1,3-dithiolane 10V, Positive-QTOFsplash10-00di-1900000000-270bdbc132a5335239772016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methyl-1,3-dithiolane 20V, Positive-QTOFsplash10-00fr-9600000000-cd469498fbc0e71eb0af2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methyl-1,3-dithiolane 40V, Positive-QTOFsplash10-0006-9000000000-2c22c1e30691476958632016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methyl-1,3-dithiolane 10V, Negative-QTOFsplash10-052f-9000000000-2ea3713d714bf8f9f4642016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methyl-1,3-dithiolane 20V, Negative-QTOFsplash10-0a4i-9000000000-296398224aa57bcea64d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methyl-1,3-dithiolane 40V, Negative-QTOFsplash10-0a59-9000000000-0c60bdfdf4bedd2f36f02016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methyl-1,3-dithiolane 10V, Negative-QTOFsplash10-0a4i-9000000000-655cfc70bd113b960af12021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methyl-1,3-dithiolane 20V, Negative-QTOFsplash10-052f-9000000000-b6cb2870ae74c26d24262021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methyl-1,3-dithiolane 40V, Negative-QTOFsplash10-014l-9800000000-d4d75dc6c4cb1445d0402021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methyl-1,3-dithiolane 10V, Positive-QTOFsplash10-00di-3900000000-77700f7eae688c562d082021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methyl-1,3-dithiolane 20V, Positive-QTOFsplash10-03di-9200000000-63fd31ccdb39062e420d2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methyl-1,3-dithiolane 40V, Positive-QTOFsplash10-0a4i-9000000000-4bdd61be5bd57eac4cd92021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-04FELIX labView Spectrum
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 IDFDB015033
KNApSAcK IDNot Available
Chemspider ID20518
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound21828
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1037521
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.. .