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Showing metabocard for 3,3-Dimethyl-1,2-dithiolane (HMDB0038974)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 00:19:11 UTC
Update Date2023-02-21 17:26:49 UTC
HMDB IDHMDB0038974
Secondary Accession Numbers
  • HMDB38974
Metabolite Identification
Common Name3,3-Dimethyl-1,2-dithiolane
Description3,3-Dimethyl-1,2-dithiolane belongs to the class of organic compounds known as 1,2-dithiolanes. These are organic compounds containing a 1,2-dithiolane ring. 1,2-dithiolane moiety is a 5-membered saturated aliphatic ring with three carbon atoms, and two sulfur atoms at the 1- and 2- ring positions. 3,3-Dimethyl-1,2-dithiolane has been detected, but not quantified in, a few different foods, such as arabica coffees (Coffea arabica), coffee and coffee products, and robusta coffees (Coffea canephora). This could make 3,3-dimethyl-1,2-dithiolane a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 3,3-Dimethyl-1,2-dithiolane.
Structure
Data?1677000409
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0038974 (3,3-Dimethyl-1,2-dithiolane)


  Mrv0541 02241217152D          

  7  7  0  0  0  0            999 V2000
    0.5742   -0.3690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0668    0.2869    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5742    0.9436    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2459    0.6974    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0668   -0.0406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2459   -0.1227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4100   -0.9436    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  6  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  6  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
M  END
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3D MOL for HMDB0038974 (3,3-Dimethyl-1,2-dithiolane)

HMDB0038974
     RDKit          3D
3,3-Dimethyl-1,2-dithiolane
 17 17  0  0  0  0  0  0  0  0999 V2000
   -1.3593    0.3409   -0.8906 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3264    0.2238    0.2259 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0952   -0.3354    1.4298 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8123   -0.5911   -0.1187 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9997    0.0535   -0.6338 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1735    1.7393   -0.0307 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.1497    1.8991    0.6794 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8917    0.2411   -1.8912 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9611    1.2714   -0.7958 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1111   -0.4979   -0.8224 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4136   -0.6768    2.2198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7756    0.4843    1.7507 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7596   -1.1534    1.0496 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4811   -1.3701   -0.8739 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0903   -1.2347    0.7722 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9298   -0.4976   -0.3259 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0573    0.1035   -1.7444 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  2  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  5 17  1  0
M  END
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3D SDF for HMDB0038974 (3,3-Dimethyl-1,2-dithiolane)


  Mrv0541 02241217152D          

  7  7  0  0  0  0            999 V2000
    0.5742   -0.3690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0668    0.2869    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5742    0.9436    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2459    0.6974    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0668   -0.0406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2459   -0.1227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4100   -0.9436    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  6  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  6  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0038974

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1(C)CCSS1

> <INCHI_IDENTIFIER>
InChI=1S/C5H10S2/c1-5(2)3-4-6-7-5/h3-4H2,1-2H3

> <INCHI_KEY>
LFHJFWOMFQJUBC-UHFFFAOYSA-N

> <FORMULA>
C5H10S2

> <MOLECULAR_WEIGHT>
134.263

> <EXACT_MASS>
134.0223917

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
14.45923475247923

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
2.40

> <JCHEM_LOGP>
1.8325452166666667

> <ALOGPS_LOGS>
-2.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
38.989399999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.71e-01 g/l

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

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0038974 (3,3-Dimethyl-1,2-dithiolane)

HMDB0038974
     RDKit          3D
3,3-Dimethyl-1,2-dithiolane
 17 17  0  0  0  0  0  0  0  0999 V2000
   -1.3593    0.3409   -0.8906 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3264    0.2238    0.2259 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0952   -0.3354    1.4298 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8123   -0.5911   -0.1187 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9997    0.0535   -0.6338 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1735    1.7393   -0.0307 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.1497    1.8991    0.6794 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8917    0.2411   -1.8912 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9611    1.2714   -0.7958 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1111   -0.4979   -0.8224 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4136   -0.6768    2.2198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7756    0.4843    1.7507 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7596   -1.1534    1.0496 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4811   -1.3701   -0.8739 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0903   -1.2347    0.7722 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9298   -0.4976   -0.3259 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0573    0.1035   -1.7444 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  2  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  5 17  1  0
M  END
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PDB for HMDB0038974 (3,3-Dimethyl-1,2-dithiolane)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       1.072  -0.689   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.991   0.536   0.000  0.00  0.00           C+0
HETATM    3  S   UNK     0       1.072   1.761   0.000  0.00  0.00           S+0
HETATM    4  S   UNK     0      -0.459   1.302   0.000  0.00  0.00           S+0
HETATM    5  C   UNK     0      -1.991  -0.076   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.459  -0.229   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.765  -1.761   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    6                                                       
CONECT    5    6                                                            
CONECT    6    1    4    5    7                                             
CONECT    7    6                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0038974 (3,3-Dimethyl-1,2-dithiolane)

COMPND    HMDB0038974
HETATM    1  C1  UNL     1      -1.359   0.341  -0.891  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.326   0.224   0.226  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.095  -0.335   1.430  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.812  -0.591  -0.119  1.00  0.00           C  
HETATM    5  C5  UNL     1       2.000   0.054  -0.634  1.00  0.00           C  
HETATM    6  S1  UNL     1       2.173   1.739  -0.031  1.00  0.00           S  
HETATM    7  S2  UNL     1       0.150   1.899   0.679  1.00  0.00           S  
HETATM    8  H1  UNL     1      -0.892   0.241  -1.891  1.00  0.00           H  
HETATM    9  H2  UNL     1      -1.961   1.271  -0.796  1.00  0.00           H  
HETATM   10  H3  UNL     1      -2.111  -0.498  -0.822  1.00  0.00           H  
HETATM   11  H4  UNL     1      -0.414  -0.677   2.220  1.00  0.00           H  
HETATM   12  H5  UNL     1      -1.776   0.484   1.751  1.00  0.00           H  
HETATM   13  H6  UNL     1      -1.760  -1.153   1.050  1.00  0.00           H  
HETATM   14  H7  UNL     1       0.481  -1.370  -0.874  1.00  0.00           H  
HETATM   15  H8  UNL     1       1.090  -1.235   0.772  1.00  0.00           H  
HETATM   16  H9  UNL     1       2.930  -0.498  -0.326  1.00  0.00           H  
HETATM   17  H10 UNL     1       2.057   0.104  -1.744  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    4    7
CONECT    3   11   12   13
CONECT    4    5   14   15
CONECT    5    6   16   17
CONECT    6    7
END
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SMILES for HMDB0038974 (3,3-Dimethyl-1,2-dithiolane)

CC1(C)CCSS1
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INCHI for HMDB0038974 (3,3-Dimethyl-1,2-dithiolane)

InChI=1S/C5H10S2/c1-5(2)3-4-6-7-5/h3-4H2,1-2H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2,5-Dimethoxy-thiopheneHMDB
Chemical FormulaC5H10S2
Average Molecular Weight134.263
Monoisotopic Molecular Weight134.0223917
IUPAC Name3,3-dimethyl-1,2-dithiolane
Traditional Name3,3-dimethyl-1,2-dithiolane
CAS Registry Number58384-57-9
SMILES
CC1(C)CCSS1
InChI Identifier
InChI=1S/C5H10S2/c1-5(2)3-4-6-7-5/h3-4H2,1-2H3
InChI KeyLFHJFWOMFQJUBC-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 1,2-dithiolanes. These are organic compounds containing a 1,2-dithiolane ring. 1,2-Dithiolane moiety is a 5-membered saturated aliphatic ring with three carbon atoms, and two sulfur atoms at the 1- and 2- ring positions.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDithiolanes
Sub Class1,2-dithiolanes
Direct Parent1,2-dithiolanes
Alternative Parents
Substituents
  • 1,2-dithiolane
  • Organic disulfide
  • Hydrocarbon derivative
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point164.00 to 165.00 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility190.3 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP2.921 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.37 g/LALOGPS
logP2.4ALOGPS
logP1.83ChemAxon
logS-2.6ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity38.99 m³·mol⁻¹ChemAxon
Polarizability14.46 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]+126.62331661259
DarkChem[M-H]-121.33331661259
DeepCCS[M+H]+133.52930932474
DeepCCS[M-H]-131.37430932474
DeepCCS[M-2H]-167.11730932474
DeepCCS[M+Na]+141.97530932474
AllCCS[M+H]+122.232859911
AllCCS[M+H-H2O]+117.632859911
AllCCS[M+NH4]+126.532859911
AllCCS[M+Na]+127.732859911
AllCCS[M-H]-131.232859911
AllCCS[M+Na-2H]-134.432859911
AllCCS[M+HCOO]-138.032859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3,3-Dimethyl-1,2-dithiolaneCC1(C)CCSS11454.4Standard polar33892256
3,3-Dimethyl-1,2-dithiolaneCC1(C)CCSS11022.7Standard non polar33892256
3,3-Dimethyl-1,2-dithiolaneCC1(C)CCSS11054.3Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3,3-Dimethyl-1,2-dithiolane GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9200000000-bcda88d541a69e17030f2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3,3-Dimethyl-1,2-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 - 3,3-Dimethyl-1,2-dithiolane 10V, Positive-QTOFsplash10-000i-0900000000-a200a10140041780324f2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,3-Dimethyl-1,2-dithiolane 20V, Positive-QTOFsplash10-000i-2900000000-6d2c7d16e307f22612242015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,3-Dimethyl-1,2-dithiolane 40V, Positive-QTOFsplash10-0gbi-9200000000-b0eddb30bb7f8a547f692015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,3-Dimethyl-1,2-dithiolane 10V, Negative-QTOFsplash10-00lr-9700000000-0aa7b09b08dde72aa86a2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,3-Dimethyl-1,2-dithiolane 20V, Negative-QTOFsplash10-00kb-9200000000-3e81ddd443d0b69184592015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,3-Dimethyl-1,2-dithiolane 40V, Negative-QTOFsplash10-0ab9-9100000000-ee3962e3ec865ad665082015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,3-Dimethyl-1,2-dithiolane 10V, Negative-QTOFsplash10-001i-0900000000-8253c37b254e05d8da342021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,3-Dimethyl-1,2-dithiolane 20V, Negative-QTOFsplash10-01x0-9500000000-c0a16d3a8b5aa3263f4c2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,3-Dimethyl-1,2-dithiolane 40V, Negative-QTOFsplash10-001i-0900000000-7b8a56ce4fe42beca9942021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,3-Dimethyl-1,2-dithiolane 10V, Positive-QTOFsplash10-0f79-2900000000-e8286f6c22830b80e8fc2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,3-Dimethyl-1,2-dithiolane 20V, Positive-QTOFsplash10-002f-9100000000-3080c3df811f41597d982021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3,3-Dimethyl-1,2-dithiolane 40V, Positive-QTOFsplash10-0adi-9000000000-8dc7453f22783ddd5b512021-09-25Wishart LabView Spectrum

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 IDFDB018460
KNApSAcK IDNot Available
Chemspider ID4955984
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound6453614
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1543901
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.. .