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Showing metabocard for 2-Vinyl-4H-1,3-dithiine (HMDB0034901)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 19:49:48 UTC
Update Date2023-02-21 17:24:29 UTC
HMDB IDHMDB0034901
Secondary Accession Numbers
  • HMDB34901
Metabolite Identification
Common Name2-Vinyl-4H-1,3-dithiine
Description2-Vinyl-4H-1,3-dithiine belongs to the class of organic compounds known as dithiins. Dithiins are compounds comprising a dithiin ring, which is an unsaturated six-member heterocycle containing four carbon atoms, two sulfur atoms and two double bonds. 2-Vinyl-4H-1,3-dithiine is found, on average, in the highest concentration within soft-necked garlics (Allium sativum L. var. sativum). 2-Vinyl-4H-1,3-dithiine has also been detected, but not quantified in, several different foods, such as garden onions (Allium cepa), green onion, garlics (Allium sativum), onion-family vegetables, and garden onion (var.). This could make 2-vinyl-4H-1,3-dithiine a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 2-Vinyl-4H-1,3-dithiine.
Structure
Data?1677000269
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0034901 (2-Vinyl-4H-1,3-dithiine)


  Mrv0541 05061308082D          

  8  8  0  0  0  0            999 V2000
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  4  3  2  0  0  0  0
  5  3  1  0  0  0  0
  6  2  1  0  0  0  0
  7  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  5  1  0  0  0  0
  8  6  1  0  0  0  0
M  END
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3D MOL for HMDB0034901 (2-Vinyl-4H-1,3-dithiine)

HMDB0034901
     RDKit          3D
2-Vinyl-4H-1,3-dithiine
 16 16  0  0  0  0  0  0  0  0999 V2000
    2.9298    0.4745   -0.3088 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1404   -0.5765   -0.1622 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7450   -0.5205   -0.6643 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0948    1.1634   -0.6827 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3537    1.3858    0.2947 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2692    0.4563    0.5432 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0655   -0.9077   -0.0534 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3778   -1.5066    0.3603 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.5624    1.3848   -0.7972 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9575    0.5048    0.0325 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4785   -1.4681    0.3086 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7068   -0.9749   -1.6941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5519    2.3700    0.7575 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1329    0.6484    1.1460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1075   -0.7866   -1.1559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7566   -1.6473    0.3402 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  3  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  5 13  1  0
  6 14  1  0
  7 15  1  0
  7 16  1  0
M  END
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3D SDF for HMDB0034901 (2-Vinyl-4H-1,3-dithiine)


  Mrv0541 05061308082D          

  8  8  0  0  0  0            999 V2000
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  4  3  2  0  0  0  0
  5  3  1  0  0  0  0
  6  2  1  0  0  0  0
  7  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  5  1  0  0  0  0
  8  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0034901

> <DATABASE_NAME>
hmdb

> <SMILES>
C=CC1SCC=CS1

> <INCHI_IDENTIFIER>
InChI=1S/C6H8S2/c1-2-6-7-4-3-5-8-6/h2-4,6H,1,5H2

> <INCHI_KEY>
XUKBDTUPIIADOP-UHFFFAOYSA-N

> <FORMULA>
C6H8S2

> <MOLECULAR_WEIGHT>
144.258

> <EXACT_MASS>
144.006741636

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
15.312353521216645

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-ethenyl-2,4-dihydro-1,3-dithiine

> <ALOGPS_LOGP>
2.10

> <JCHEM_LOGP>
2.374465655333333

> <ALOGPS_LOGS>
-2.97

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
43.2234

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.56e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-ethenyl-2,4-dihydro-1,3-dithiine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0034901 (2-Vinyl-4H-1,3-dithiine)

HMDB0034901
     RDKit          3D
2-Vinyl-4H-1,3-dithiine
 16 16  0  0  0  0  0  0  0  0999 V2000
    2.9298    0.4745   -0.3088 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1404   -0.5765   -0.1622 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7450   -0.5205   -0.6643 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0948    1.1634   -0.6827 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3537    1.3858    0.2947 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2692    0.4563    0.5432 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0655   -0.9077   -0.0534 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3778   -1.5066    0.3603 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.5624    1.3848   -0.7972 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9575    0.5048    0.0325 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4785   -1.4681    0.3086 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7068   -0.9749   -1.6941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5519    2.3700    0.7575 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1329    0.6484    1.1460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1075   -0.7866   -1.1559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7566   -1.6473    0.3402 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  3  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  5 13  1  0
  6 14  1  0
  7 15  1  0
  7 16  1  0
M  END
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PDB for HMDB0034901 (2-Vinyl-4H-1,3-dithiine)

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       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    7  S   UNK     0       2.667   1.540   0.000  0.00  0.00           S+0
HETATM    8  S   UNK     0       0.000   1.540   0.000  0.00  0.00           S+0
CONECT    1    2                                                            
CONECT    2    1    6                                                       
CONECT    3    4    5                                                       
CONECT    4    3    7                                                       
CONECT    5    3    8                                                       
CONECT    6    2    7    8                                                  
CONECT    7    4    6                                                       
CONECT    8    5    6                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0034901 (2-Vinyl-4H-1,3-dithiine)

COMPND    HMDB0034901
HETATM    1  C1  UNL     1       2.930   0.475  -0.309  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.140  -0.576  -0.162  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.745  -0.521  -0.664  1.00  0.00           C  
HETATM    4  S1  UNL     1       0.095   1.163  -0.683  1.00  0.00           S  
HETATM    5  C4  UNL     1      -1.354   1.386   0.295  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.269   0.456   0.543  1.00  0.00           C  
HETATM    7  C6  UNL     1      -2.066  -0.908  -0.053  1.00  0.00           C  
HETATM    8  S2  UNL     1      -0.378  -1.507   0.360  1.00  0.00           S  
HETATM    9  H1  UNL     1       2.562   1.385  -0.797  1.00  0.00           H  
HETATM   10  H2  UNL     1       3.957   0.505   0.033  1.00  0.00           H  
HETATM   11  H3  UNL     1       2.478  -1.468   0.309  1.00  0.00           H  
HETATM   12  H4  UNL     1       0.707  -0.975  -1.694  1.00  0.00           H  
HETATM   13  H5  UNL     1      -1.552   2.370   0.758  1.00  0.00           H  
HETATM   14  H6  UNL     1      -3.133   0.648   1.146  1.00  0.00           H  
HETATM   15  H7  UNL     1      -2.108  -0.787  -1.156  1.00  0.00           H  
HETATM   16  H8  UNL     1      -2.757  -1.647   0.340  1.00  0.00           H  
CONECT    1    2    2    9   10
CONECT    2    3   11
CONECT    3    4    8   12
CONECT    4    5
CONECT    5    6    6   13
CONECT    6    7   14
CONECT    7    8   15   16
END
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SMILES for HMDB0034901 (2-Vinyl-4H-1,3-dithiine)

C=CC1SCC=CS1
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INCHI for HMDB0034901 (2-Vinyl-4H-1,3-dithiine)

InChI=1S/C6H8S2/c1-2-6-7-4-3-5-8-6/h2-4,6H,1,5H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1-Ethyltridecyl 3-bromobenzoateHMDB
2-Ethenyl-4H-1,3-dithiinHMDB
2-Ethenyl-4H-1,3-dithiine, 9ciHMDB
2-VdtiiHMDB
2-Vinyl-(4H)-1,3-dithiineHMDB
2-Vinyl-4(H)-1,3-dithiinHMDB
2-Vinyl-4H-1,3-dithiinHMDB
2-Vinyl-4H-1,3-dithinHMDB
2-Vinyl-[4H]-1,3-dithinHMDB
3-Bromobenzoic acid, 3-pentadecyl esterHMDB
4H-1,3-Dithiin, 2-ethenylHMDB
Chemical FormulaC6H8S2
Average Molecular Weight144.258
Monoisotopic Molecular Weight144.006741636
IUPAC Name2-ethenyl-2,4-dihydro-1,3-dithiine
Traditional Name2-ethenyl-2,4-dihydro-1,3-dithiine
CAS Registry Number80028-57-5
SMILES
C=CC1SCC=CS1
InChI Identifier
InChI=1S/C6H8S2/c1-2-6-7-4-3-5-8-6/h2-4,6H,1,5H2
InChI KeyXUKBDTUPIIADOP-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dithiins. Dithiins are compounds comprising a dithiin ring, which is an unsaturated six-member heterocycle containing four carbon atoms, two sulfur atoms and two double bonds.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDithiins
Sub ClassNot Available
Direct ParentDithiins
Alternative Parents
Substituents
  • 1,3-dithiin
  • Thioacetal
  • Thioenolether
  • Dialkylthioether
  • Thioether
  • Hydrocarbon derivative
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological roleIndustrial application
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility203.9 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.16 g/LALOGPS
logP2.1ALOGPS
logP2.37ChemAxon
logS-3ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity43.22 m³·mol⁻¹ChemAxon
Polarizability15.31 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]+127.4431661259
DarkChem[M-H]-123.14431661259
DeepCCS[M+H]+131.00930932474
DeepCCS[M-H]-128.94630932474
DeepCCS[M-2H]-164.5130932474
DeepCCS[M+Na]+138.7830932474
AllCCS[M+H]+125.932859911
AllCCS[M+H-H2O]+121.332859911
AllCCS[M+NH4]+130.132859911
AllCCS[M+Na]+131.432859911
AllCCS[M-H]-129.232859911
AllCCS[M+Na-2H]-131.832859911
AllCCS[M+HCOO]-134.632859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-Vinyl-4H-1,3-dithiineC=CC1SCC=CS11872.6Standard polar33892256
2-Vinyl-4H-1,3-dithiineC=CC1SCC=CS11168.1Standard non polar33892256
2-Vinyl-4H-1,3-dithiineC=CC1SCC=CS11197.1Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 2-Vinyl-4H-1,3-dithiine GC-MS (Non-derivatized) - 70eV, Positivesplash10-0076-9300000000-427ec03e23132d179c772017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Vinyl-4H-1,3-dithiine 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-Vinyl-4H-1,3-dithiine 10V, Positive-QTOFsplash10-0002-0900000000-3e4031f35064cbb84c6c2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Vinyl-4H-1,3-dithiine 20V, Positive-QTOFsplash10-0002-9400000000-3f55c8c9bcb5d7f640b82016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Vinyl-4H-1,3-dithiine 40V, Positive-QTOFsplash10-00di-9200000000-b8c078f742906e31bf232016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Vinyl-4H-1,3-dithiine 10V, Negative-QTOFsplash10-0k97-7900000000-d5450a6d81360c9060b72016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Vinyl-4H-1,3-dithiine 20V, Negative-QTOFsplash10-00di-9000000000-4f1ad5366369dc5b28f92016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Vinyl-4H-1,3-dithiine 40V, Negative-QTOFsplash10-00di-9000000000-63208c7fa296fbcdcd5a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Vinyl-4H-1,3-dithiine 10V, Negative-QTOFsplash10-006x-5900000000-aee8163659956229a8872021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Vinyl-4H-1,3-dithiine 20V, Negative-QTOFsplash10-00dl-9400000000-990c5bd04132b963aca62021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Vinyl-4H-1,3-dithiine 40V, Negative-QTOFsplash10-00dl-9800000000-4bcdcb7bb21fc0af60752021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Vinyl-4H-1,3-dithiine 10V, Positive-QTOFsplash10-0002-3900000000-e3821642d6b887647ed22021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Vinyl-4H-1,3-dithiine 20V, Positive-QTOFsplash10-007a-9200000000-27e6f3875eaaa018745f2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Vinyl-4H-1,3-dithiine 40V, Positive-QTOFsplash10-05g0-9000000000-f8425ec58d9ee201de032021-09-24Wishart 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 IDFDB013480
KNApSAcK IDC00058205
Chemspider ID117630
KEGG Compound IDNot Available
BioCyc IDCPD-9295
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound133337
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1846241
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.. .