Hmdb loader

Showing metabocard for 3-Vinyl-1,2-dithiacyclohex-4-ene (HMDB0302176)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-23 15:16:36 UTC
Update Date2021-09-23 15:16:36 UTC
HMDB IDHMDB0302176
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-Vinyl-1,2-dithiacyclohex-4-ene
Description3-vinyl-1,2-dithiacyclohex-4-ene is a member of the class of 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. 3-vinyl-1,2-dithiacyclohex-4-ene can be found in soft-necked garlic, which makes 3-vinyl-1,2-dithiacyclohex-4-ene a potential biomarker for the consumption of this food product.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0302176 (3-Vinyl-1,2-dithiacyclohex-4-ene)


  Mrv0541 02241221262D          

  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    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    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
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  3  8  1  0  0  0  0
M  END
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3D MOL for HMDB0302176 (3-Vinyl-1,2-dithiacyclohex-4-ene)

HMDB0302176
     RDKit          3D
3-Vinyl-1,2-dithiacyclohex-4-ene
 16 16  0  0  0  0  0  0  0  0999 V2000
    2.7044    0.1706   -0.5759 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5823   -0.4845   -0.8130 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5792   -0.6746    0.3023 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1845    0.5670    0.4314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4017    0.8749    0.1200 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4760    0.0821   -0.4850 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9512   -1.4290   -1.3253 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3570   -2.1564   -0.1132 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.4298    0.3135   -1.3642 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9607    0.5923    0.3911 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4258   -0.8639   -1.8121 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1346   -0.8313    1.2726 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4313    1.3962    0.8913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7246    1.9317    0.3460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2202   -0.2350    0.2766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9327    0.7466   -1.2546 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  2  0
  5  6  1  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
  4 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
M  END
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3D SDF for HMDB0302176 (3-Vinyl-1,2-dithiacyclohex-4-ene)


  Mrv0541 02241221262D          

  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    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    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
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  3  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0302176

> <DATABASE_NAME>
hmdb

> <SMILES>
C=CC1SSCC=C1

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

> <INCHI_KEY>
UQXHSMWBRGWFBK-UHFFFAOYSA-N

> <FORMULA>
C6H8S2

> <MOLECULAR_WEIGHT>
144.258

> <EXACT_MASS>
144.006741636

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
15.147372895715527

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-ethenyl-3,6-dihydro-1,2-dithiine

> <ALOGPS_LOGP>
2.31

> <JCHEM_LOGP>
2.419490585666667

> <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>
44.246300000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.54e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-ethenyl-3,6-dihydro-1,2-dithiine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0302176 (3-Vinyl-1,2-dithiacyclohex-4-ene)

HMDB0302176
     RDKit          3D
3-Vinyl-1,2-dithiacyclohex-4-ene
 16 16  0  0  0  0  0  0  0  0999 V2000
    2.7044    0.1706   -0.5759 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5823   -0.4845   -0.8130 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5792   -0.6746    0.3023 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1845    0.5670    0.4314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4017    0.8749    0.1200 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4760    0.0821   -0.4850 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9512   -1.4290   -1.3253 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3570   -2.1564   -0.1132 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.4298    0.3135   -1.3642 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9607    0.5923    0.3911 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4258   -0.8639   -1.8121 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1346   -0.8313    1.2726 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4313    1.3962    0.8913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7246    1.9317    0.3460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2202   -0.2350    0.2766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9327    0.7466   -1.2546 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  2  0
  5  6  1  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
  4 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
M  END
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PDB for HMDB0302176 (3-Vinyl-1,2-dithiacyclohex-4-ene)

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       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   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  S   UNK     0       0.000   0.000   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    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    3                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0302176 (3-Vinyl-1,2-dithiacyclohex-4-ene)

COMPND    HMDB0302176
HETATM    1  C1  UNL     1       2.704   0.171  -0.576  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.582  -0.485  -0.813  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.579  -0.675   0.302  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.184   0.567   0.431  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.402   0.875   0.120  1.00  0.00           C  
HETATM    6  C6  UNL     1      -2.476   0.082  -0.485  1.00  0.00           C  
HETATM    7  S1  UNL     1      -1.951  -1.429  -1.325  1.00  0.00           S  
HETATM    8  S2  UNL     1      -0.357  -2.156  -0.113  1.00  0.00           S  
HETATM    9  H1  UNL     1       3.430   0.313  -1.364  1.00  0.00           H  
HETATM   10  H2  UNL     1       2.961   0.592   0.391  1.00  0.00           H  
HETATM   11  H3  UNL     1       1.426  -0.864  -1.812  1.00  0.00           H  
HETATM   12  H4  UNL     1       1.135  -0.831   1.273  1.00  0.00           H  
HETATM   13  H5  UNL     1       0.431   1.396   0.891  1.00  0.00           H  
HETATM   14  H6  UNL     1      -1.725   1.932   0.346  1.00  0.00           H  
HETATM   15  H7  UNL     1      -3.220  -0.235   0.277  1.00  0.00           H  
HETATM   16  H8  UNL     1      -2.933   0.747  -1.255  1.00  0.00           H  
CONECT    1    2    2    9   10
CONECT    2    3   11
CONECT    3    4    8   12
CONECT    4    5    5   13
CONECT    5    6   14
CONECT    6    7   15   16
CONECT    7    8
END
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SMILES for HMDB0302176 (3-Vinyl-1,2-dithiacyclohex-4-ene)

C=CC1SSCC=C1
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INCHI for HMDB0302176 (3-Vinyl-1,2-dithiacyclohex-4-ene)

InChI=1S/C6H8S2/c1-2-6-4-3-5-7-8-6/h2-4,6H,1,5H2
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC6H8S2
Average Molecular Weight144.258
Monoisotopic Molecular Weight144.006741636
IUPAC Name3-ethenyl-3,6-dihydro-1,2-dithiine
Traditional Name3-ethenyl-3,6-dihydro-1,2-dithiine
CAS Registry NumberNot Available
SMILES
C=CC1SSCC=C1
InChI Identifier
InChI=1S/C6H8S2/c1-2-6-4-3-5-7-8-6/h2-4,6H,1,5H2
InChI KeyUQXHSMWBRGWFBK-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
  • 1,2-dithiin
  • Organic disulfide
  • Hydrocarbon derivative
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP2.31ALOGPS
logP2.42ChemAxon
logS-3ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity44.25 m³·mol⁻¹ChemAxon
Polarizability15.15 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
AllCCS[M+H]+125.72932859911
AllCCS[M+H-H2O]+120.98132859911
AllCCS[M+Na]+131.43932859911
AllCCS[M+NH4]+130.1632859911
AllCCS[M-H]-128.82932859911
AllCCS[M+Na-2H]-131.24432859911
AllCCS[M+HCOO]-133.94232859911
DeepCCS[M+H]+127.02330932474
DeepCCS[M-H]-124.57130932474
DeepCCS[M-2H]-160.65930932474
DeepCCS[M+Na]+135.5730932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202212.9021 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20221.15 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1720.8 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid462.2 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid183.1 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid337.2 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid161.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid463.9 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 Acid393.4 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)122.8 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1133.1 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid433.1 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1018.1 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid410.3 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid344.5 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate483.9 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA477.5 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water106.9 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Vinyl-1,2-dithiacyclohex-4-ene 10V, Positive-QTOFsplash10-0002-0900000000-cbc8a5761b122fb1089d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Vinyl-1,2-dithiacyclohex-4-ene 20V, Positive-QTOFsplash10-014j-9400000000-a07106108b444a1811ed2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Vinyl-1,2-dithiacyclohex-4-ene 40V, Positive-QTOFsplash10-00tf-9100000000-6fc974f7abac154d32132016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Vinyl-1,2-dithiacyclohex-4-ene 10V, Negative-QTOFsplash10-002f-7900000000-c9ff6f7720c6b572c2e82016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Vinyl-1,2-dithiacyclohex-4-ene 20V, Negative-QTOFsplash10-002f-9600000000-22b564b8dfe126a5f9892016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Vinyl-1,2-dithiacyclohex-4-ene 40V, Negative-QTOFsplash10-0a6r-9000000000-cf876b0ad87e4e28c1772016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Vinyl-1,2-dithiacyclohex-4-ene 10V, Positive-QTOFsplash10-0002-0900000000-5d58ed67744738ae22f92021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Vinyl-1,2-dithiacyclohex-4-ene 20V, Positive-QTOFsplash10-002b-9700000000-c60182940a2b936e4bd52021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Vinyl-1,2-dithiacyclohex-4-ene 40V, Positive-QTOFsplash10-07ku-9000000000-05b315a55f9ab1aee6b42021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Vinyl-1,2-dithiacyclohex-4-ene 10V, Negative-QTOFsplash10-0006-2900000000-5d8b3baa42764f72deb22021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Vinyl-1,2-dithiacyclohex-4-ene 20V, Negative-QTOFsplash10-0006-8900000000-f4573a0b646fd3bfb1d02021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Vinyl-1,2-dithiacyclohex-4-ene 40V, Negative-QTOFsplash10-0230-9200000000-f4d84576b3d057f465e02021-10-21Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
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 IDFDB003548
KNApSAcK IDNot Available
Chemspider ID457990
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
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References
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