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Showing metabocard for 1,3-Dithiane (HMDB0031473)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-09-11 17:43:32 UTC
Update Date2023-02-21 17:20:35 UTC
HMDB IDHMDB0031473
Secondary Accession Numbers
  • HMDB31473
Metabolite Identification
Common Name1,3-Dithiane
Description1,3-Dithiane, also known as dithiane-1,3 or m-dithiane, belongs to the class of organic compounds known as dithianes. Dithianes are compounds containing a dithiane moiety, which is composed of a cyclohexane core structure wherein two methylene units are replaced by sulfur centres. 1,3-Dithiane is an alliaceous and roasted tasting compound. 1,3-Dithiane is found, on average, in the highest concentration within soft-necked garlics (Allium sativum L. var. sativum). 1,3-Dithiane has also been detected, but not quantified in, several different foods, such as welsh onions (Allium fistulosum), onion-family vegetables, red onion, garden onion (var.), and green onion. This could make 1,3-dithiane a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on 1,3-Dithiane.
Structure
Data?1677000035
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0031473 (1,3-Dithiane)


  Mrv0541 05061305572D          

  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    0.0000    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
  2  1  1  0  0  0  0
  3  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 HMDB0031473 (1,3-Dithiane)

HMDB0031473
     RDKit          3D
1,3-Dithiane
 14 14  0  0  0  0  0  0  0  0999 V2000
   -0.9008   -0.6737   -0.0725 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9970    0.5891   -0.9047 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6864    1.2641   -1.0594 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.9194    0.1849   -0.3167 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3749   -0.4298    1.3217 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4463   -0.2321    1.3188 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1441   -1.3378   -0.5530 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8429   -1.2207    0.0044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4760    0.4187   -1.8771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6083    1.3086   -0.3000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1445   -0.6815   -0.9789 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8471    0.7490   -0.1693 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9249   -0.8009    2.1145 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6319    0.8620    1.4724 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
  4 11  1  0
  4 12  1  0
  6 13  1  0
  6 14  1  0
M  END
Download

3D SDF for HMDB0031473 (1,3-Dithiane)


  Mrv0541 05061305572D          

  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    0.0000    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
  2  1  1  0  0  0  0
  3  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>
HMDB0031473

> <DATABASE_NAME>
hmdb

> <SMILES>
C1CSCSC1

> <INCHI_IDENTIFIER>
InChI=1S/C4H8S2/c1-2-5-4-6-3-1/h1-4H2

> <INCHI_KEY>
WQADWIOXOXRPLN-UHFFFAOYSA-N

> <FORMULA>
C4H8S2

> <MOLECULAR_WEIGHT>
120.236

> <EXACT_MASS>
120.006741636

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
12.759425106985887

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,3-dithiane

> <ALOGPS_LOGP>
1.58

> <JCHEM_LOGP>
1.4980920860000002

> <ALOGPS_LOGS>
-2.04

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
34.0023

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.10e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,3-dithiane

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0031473 (1,3-Dithiane)

HMDB0031473
     RDKit          3D
1,3-Dithiane
 14 14  0  0  0  0  0  0  0  0999 V2000
   -0.9008   -0.6737   -0.0725 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9970    0.5891   -0.9047 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6864    1.2641   -1.0594 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.9194    0.1849   -0.3167 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3749   -0.4298    1.3217 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4463   -0.2321    1.3188 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1441   -1.3378   -0.5530 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8429   -1.2207    0.0044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4760    0.4187   -1.8771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6083    1.3086   -0.3000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1445   -0.6815   -0.9789 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8471    0.7490   -0.1693 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9249   -0.8009    2.1145 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6319    0.8620    1.4724 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
  4 11  1  0
  4 12  1  0
  6 13  1  0
  6 14  1  0
M  END
Download

PDB for HMDB0031473 (1,3-Dithiane)

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  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  S   UNK     0       0.000   1.540   0.000  0.00  0.00           S+0
HETATM    6  S   UNK     0       1.334  -0.770   0.000  0.00  0.00           S+0
CONECT    1    2    3                                                       
CONECT    2    1    5                                                       
CONECT    3    1    6                                                       
CONECT    4    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 HMDB0031473 (1,3-Dithiane)

COMPND    HMDB0031473
HETATM    1  C1  UNL     1      -0.901  -0.674  -0.073  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.997   0.589  -0.905  1.00  0.00           C  
HETATM    3  S1  UNL     1       0.686   1.264  -1.059  1.00  0.00           S  
HETATM    4  C3  UNL     1       1.919   0.185  -0.317  1.00  0.00           C  
HETATM    5  S2  UNL     1       1.375  -0.430   1.322  1.00  0.00           S  
HETATM    6  C4  UNL     1      -0.446  -0.232   1.319  1.00  0.00           C  
HETATM    7  H1  UNL     1      -0.144  -1.338  -0.553  1.00  0.00           H  
HETATM    8  H2  UNL     1      -1.843  -1.221   0.004  1.00  0.00           H  
HETATM    9  H3  UNL     1      -1.476   0.419  -1.877  1.00  0.00           H  
HETATM   10  H4  UNL     1      -1.608   1.309  -0.300  1.00  0.00           H  
HETATM   11  H5  UNL     1       2.144  -0.681  -0.979  1.00  0.00           H  
HETATM   12  H6  UNL     1       2.847   0.749  -0.169  1.00  0.00           H  
HETATM   13  H7  UNL     1      -0.925  -0.801   2.114  1.00  0.00           H  
HETATM   14  H8  UNL     1      -0.632   0.862   1.472  1.00  0.00           H  
CONECT    1    2    6    7    8
CONECT    2    3    9   10
CONECT    3    4
CONECT    4    5   11   12
CONECT    5    6
CONECT    6   13   14
END
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SMILES for HMDB0031473 (1,3-Dithiane)

C1CSCSC1
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INCHI for HMDB0031473 (1,3-Dithiane)

InChI=1S/C4H8S2/c1-2-5-4-6-3-1/h1-4H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1,3-DithiacyclohexaneChEBI
1,3-DithianChEBI
Dithiane-1,3ChEBI
m-DithianeChEBI
1,3 DithiocyclohexaneHMDB
m-Dithiane, 8ciHMDB
Chemical FormulaC4H8S2
Average Molecular Weight120.236
Monoisotopic Molecular Weight120.006741636
IUPAC Name1,3-dithiane
Traditional Name1,3-dithiane
CAS Registry Number505-23-7
SMILES
C1CSCSC1
InChI Identifier
InChI=1S/C4H8S2/c1-2-5-4-6-3-1/h1-4H2
InChI KeyWQADWIOXOXRPLN-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dithianes. Dithianes are compounds containing a dithiane moiety, which is composed of a cyclohexane core structure wherein two methylene units are replaced by sulfur centres.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDithianes
Sub ClassNot Available
Direct ParentDithianes
Alternative Parents
Substituents
  • 1,3-dithiane
  • Thioacetal
  • Dialkylthioether
  • Thioether
  • Hydrocarbon derivative
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point54 °CNot Available
Boiling Point195.00 to 196.00 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility1384 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP1.729 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility1.1 g/LALOGPS
logP1.58ALOGPS
logP1.5ChemAxon
logS-2ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity34 m³·mol⁻¹ChemAxon
Polarizability12.76 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]+121.02731661259
DarkChem[M-H]-115.58131661259
DeepCCS[M+H]+130.91730932474
DeepCCS[M-H]-128.82230932474
DeepCCS[M-2H]-164.33730932474
DeepCCS[M+Na]+138.95230932474
AllCCS[M+H]+120.132859911
AllCCS[M+H-H2O]+115.232859911
AllCCS[M+NH4]+124.632859911
AllCCS[M+Na]+125.932859911
AllCCS[M-H]-132.932859911
AllCCS[M+Na-2H]-136.732859911
AllCCS[M+HCOO]-140.832859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
1,3-DithianeC1CSCSC11415.5Standard polar33892256
1,3-DithianeC1CSCSC11059.8Standard non polar33892256
1,3-DithianeC1CSCSC11096.8Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 1,3-Dithiane GC-MS (Non-derivatized) - 70eV, Positivesplash10-006x-9100000000-dacbe5356974035578032017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1,3-Dithiane 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 - 1,3-Dithiane 10V, Positive-QTOFsplash10-00di-0900000000-cdb9343612b598c4b21a2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dithiane 20V, Positive-QTOFsplash10-006x-9200000000-92e7461dacc7b4461e872015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dithiane 40V, Positive-QTOFsplash10-004i-9000000000-534d44f8a83e1f9a5d832015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dithiane 10V, Negative-QTOFsplash10-00di-9300000000-7114756b0ee71b7e4ade2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dithiane 20V, Negative-QTOFsplash10-00di-9000000000-f92e4d4f533cf6199bf42015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dithiane 40V, Negative-QTOFsplash10-00e9-9000000000-96b1eb41edf0e867d8082015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dithiane 10V, Negative-QTOFsplash10-014i-0900000000-32521afe640ff743a0982021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dithiane 20V, Negative-QTOFsplash10-016r-4900000000-fd6fc020260f8f5db3072021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dithiane 40V, Negative-QTOFsplash10-014i-2900000000-74b936565a210812f4502021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dithiane 10V, Positive-QTOFsplash10-00di-0900000000-c08ad45f468b2367fa172021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dithiane 20V, Positive-QTOFsplash10-022i-9200000000-ebf741fd3c608a3f558a2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dithiane 40V, Positive-QTOFsplash10-0002-9000000000-8c02da8f5d5b26294be72021-09-24Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-03FELIX labView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen Locations
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB008046
KNApSAcK IDNot Available
Chemspider ID10019
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10451
PDB IDNot Available
ChEBI ID47845
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1147821
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.. .