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Showing metabocard for 1,2,3-Trithiane (HMDB0040452)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 01:59:36 UTC
Update Date2023-02-21 17:28:17 UTC
HMDB IDHMDB0040452
Secondary Accession Numbers
  • HMDB40452
Metabolite Identification
Common Name1,2,3-Trithiane
Description1,2,3-Trithiane belongs to the class of organic compounds known as trithianes. These are organic compounds containing a six-member aliphatic saturated heterocycle made up of three sulfur atoms and three carbon atoms. 1,2,3-Trithiane has been detected, but not quantified in, several different foods, such as garden onion (var.), welsh onions (Allium fistulosum), onion-family vegetables, green onion, and garden onions (Allium cepa). This could make 1,2,3-trithiane a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 1,2,3-Trithiane.
Structure
Data?1677000497
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0040452 (1,2,3-Trithiane)


  Mrv0541 05061311512D          

  6  6  0  0  0  0            999 V2000
    1.4289    0.8250    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    0.0000    0.0000 C   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
    0.7145   -0.4125    0.0000 S   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
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
M  END
Download

3D MOL for HMDB0040452 (1,2,3-Trithiane)

HMDB0040452
     RDKit          3D
1,2,3-Trithiane
 12 12  0  0  0  0  0  0  0  0999 V2000
   -0.6884    0.2328   -0.3666 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4944   -1.2005   -0.0600 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0885   -1.6360    0.6404 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.5959   -0.4630   -0.3568 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.6902    1.4949   -0.4089 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0946    1.1898    0.4536 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7813    0.4732   -0.2096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5044    0.4616   -1.4396 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6293   -1.8084   -1.0001 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2967   -1.5820    0.6267 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3297    0.7035    1.4343 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4044    2.1340    0.6865 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  1  1  0
  1  7  1  0
  1  8  1  0
  2  9  1  0
  2 10  1  0
  6 11  1  0
  6 12  1  0
M  END
Download

3D SDF for HMDB0040452 (1,2,3-Trithiane)


  Mrv0541 05061311512D          

  6  6  0  0  0  0            999 V2000
    1.4289    0.8250    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    0.0000    0.0000 C   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
    0.7145   -0.4125    0.0000 S   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
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0040452

> <DATABASE_NAME>
hmdb

> <SMILES>
C1CSSSC1

> <INCHI_IDENTIFIER>
InChI=1S/C3H6S3/c1-2-4-6-5-3-1/h1-3H2

> <INCHI_KEY>
BVOMRRWJQOJMPA-UHFFFAOYSA-N

> <FORMULA>
C3H6S3

> <MOLECULAR_WEIGHT>
138.275

> <EXACT_MASS>
137.963162262

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
13.313726431738012

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,2,3-trithiane

> <ALOGPS_LOGP>
1.49

> <JCHEM_LOGP>
1.7814405359999999

> <ALOGPS_LOGS>
-2.06

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
35.7438

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.21e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,2,3-trithiane

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0040452 (1,2,3-Trithiane)

HMDB0040452
     RDKit          3D
1,2,3-Trithiane
 12 12  0  0  0  0  0  0  0  0999 V2000
   -0.6884    0.2328   -0.3666 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4944   -1.2005   -0.0600 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0885   -1.6360    0.6404 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.5959   -0.4630   -0.3568 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.6902    1.4949   -0.4089 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0946    1.1898    0.4536 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7813    0.4732   -0.2096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5044    0.4616   -1.4396 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6293   -1.8084   -1.0001 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2967   -1.5820    0.6267 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3297    0.7035    1.4343 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4044    2.1340    0.6865 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  1  1  0
  1  7  1  0
  1  8  1  0
  2  9  1  0
  2 10  1  0
  6 11  1  0
  6 12  1  0
M  END
Download

PDB for HMDB0040452 (1,2,3-Trithiane)

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       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    4  S   UNK     0       0.000   1.540   0.000  0.00  0.00           S+0
HETATM    5  S   UNK     0       1.334  -0.770   0.000  0.00  0.00           S+0
HETATM    6  S   UNK     0       0.000   0.000   0.000  0.00  0.00           S+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    6                                                       
CONECT    6    4    5                                                       
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
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3D PDB for HMDB0040452 (1,2,3-Trithiane)

COMPND    HMDB0040452
HETATM    1  C1  UNL     1      -0.688   0.233  -0.367  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.494  -1.200  -0.060  1.00  0.00           C  
HETATM    3  S1  UNL     1       1.089  -1.636   0.640  1.00  0.00           S  
HETATM    4  S2  UNL     1       2.596  -0.463  -0.357  1.00  0.00           S  
HETATM    5  S3  UNL     1       1.690   1.495  -0.409  1.00  0.00           S  
HETATM    6  C3  UNL     1       0.095   1.190   0.454  1.00  0.00           C  
HETATM    7  H1  UNL     1      -1.781   0.473  -0.210  1.00  0.00           H  
HETATM    8  H2  UNL     1      -0.504   0.462  -1.440  1.00  0.00           H  
HETATM    9  H3  UNL     1      -0.629  -1.808  -1.000  1.00  0.00           H  
HETATM   10  H4  UNL     1      -1.297  -1.582   0.627  1.00  0.00           H  
HETATM   11  H5  UNL     1       0.330   0.704   1.434  1.00  0.00           H  
HETATM   12  H6  UNL     1      -0.404   2.134   0.686  1.00  0.00           H  
CONECT    1    2    6    7    8
CONECT    2    3    9   10
CONECT    3    4
CONECT    4    5
CONECT    5    6
CONECT    6   11   12
END
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SMILES for HMDB0040452 (1,2,3-Trithiane)

C1CSSSC1
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INCHI for HMDB0040452 (1,2,3-Trithiane)

InChI=1S/C3H6S3/c1-2-4-6-5-3-1/h1-3H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1,2,3-TrithiacyclohexaneChEBI
1,2,3-TrithianChEBI
N-Trithiane, 8ciHMDB
Chemical FormulaC3H6S3
Average Molecular Weight138.275
Monoisotopic Molecular Weight137.963162262
IUPAC Name1,2,3-trithiane
Traditional Name1,2,3-trithiane
CAS Registry Number3325-33-5
SMILES
C1CSSSC1
InChI Identifier
InChI=1S/C3H6S3/c1-2-4-6-5-3-1/h1-3H2
InChI KeyBVOMRRWJQOJMPA-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as trithianes. These are organic compounds containing a six-member aliphatic saturated heterocycle made up of three sulfur atoms and three carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassTrithianes
Sub ClassNot Available
Direct ParentTrithianes
Alternative Parents
Substituents
  • Trithiane
  • Organic trisulfide
  • Hydrocarbon derivative
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point46 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility1016 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility1.21 g/LALOGPS
logP1.49ALOGPS
logP1.78ChemAxon
logS-2.1ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity35.74 m³·mol⁻¹ChemAxon
Polarizability13.31 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]+124.44931661259
DarkChem[M-H]-119.05831661259
DeepCCS[M+H]+127.86130932474
DeepCCS[M-H]-125.87830932474
DeepCCS[M-2H]-161.29930932474
DeepCCS[M+Na]+135.8530932474
AllCCS[M+H]+123.732859911
AllCCS[M+H-H2O]+118.932859911
AllCCS[M+NH4]+128.132859911
AllCCS[M+Na]+129.432859911
AllCCS[M-H]-134.132859911
AllCCS[M+Na-2H]-137.832859911
AllCCS[M+HCOO]-141.932859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
1,2,3-TrithianeC1CSSSC11660.8Standard polar33892256
1,2,3-TrithianeC1CSSSC11181.0Standard non polar33892256
1,2,3-TrithianeC1CSSSC11233.7Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 1,2,3-Trithiane GC-MS (Non-derivatized) - 70eV, Positivesplash10-000f-9300000000-19fe8a479208b854c87e2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1,2,3-Trithiane 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 - 1,2,3-Trithiane 10V, Positive-QTOFsplash10-000i-0900000000-358ae177078fb17accec2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,2,3-Trithiane 20V, Positive-QTOFsplash10-08fu-9100000000-202d6ac772a3d9b018b12017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,2,3-Trithiane 40V, Positive-QTOFsplash10-002f-9100000000-d8e3cafe944b0cba5b542017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,2,3-Trithiane 10V, Negative-QTOFsplash10-0079-9700000000-e68ebdb971142fe9a7f92017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,2,3-Trithiane 20V, Negative-QTOFsplash10-00di-9000000000-521469b20a99dce123892017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,2,3-Trithiane 40V, Negative-QTOFsplash10-03di-9000000000-aab6ab19760bc5dd70ee2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,2,3-Trithiane 10V, Negative-QTOFsplash10-0udi-0900000000-b2acdb1b7fceb72b06572021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,2,3-Trithiane 20V, Negative-QTOFsplash10-03dr-9800000000-a333429d5930d9f8e3902021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,2,3-Trithiane 40V, Negative-QTOFsplash10-01p9-8900000000-676068713511919c5a112021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,2,3-Trithiane 10V, Positive-QTOFsplash10-000i-0900000000-647654a04a1b7eb294f22021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,2,3-Trithiane 20V, Positive-QTOFsplash10-0h73-9400000000-0d7bd3251aeecd6599132021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,2,3-Trithiane 40V, Positive-QTOFsplash10-0006-9000000000-208cc109b7b942ec41a12021-09-22Wishart 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 IDFDB020205
KNApSAcK IDC00058084
Chemspider ID109801
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound123186
PDB IDNot Available
ChEBI ID39194
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1883411
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.. .