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Showing metabocard for 2,5-Dimethyltetrahydrothiophene (HMDB0302173)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-23 15:15:11 UTC
Update Date2021-09-23 15:15:12 UTC
HMDB IDHMDB0302173
Secondary Accession NumbersNone
Metabolite Identification
Common Name2,5-Dimethyltetrahydrothiophene
Description2,5-dimethyltetrahydrothiophene is a member of the class of compounds known as thiolanes. Thiolanes are organic compounds containing thiolane, a five-member saturated ring containing four carbon atoms and a sulfur atom. 2,5-dimethyltetrahydrothiophene can be found in soft-necked garlic, which makes 2,5-dimethyltetrahydrothiophene a potential biomarker for the consumption of this food product.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0302173 (2,5-Dimethyltetrahydrothiophene)


  Mrv1533007131513272D          

  7  7  0  0  0  0            999 V2000
   -0.3297   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  5  3  1  0  0  0  0
  6  2  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  7  6  1  0  0  0  0
M  END
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3D MOL for HMDB0302173 (2,5-Dimethyltetrahydrothiophene)

HMDB0302173
     RDKit          3D
2,5-Dimethyltetrahydrothiophene
 19 19  0  0  0  0  0  0  0  0999 V2000
   -2.1488   -0.8329    0.6375 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3555   -0.6334   -0.6079 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9350    0.7713   -0.8687 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3678    1.0207   -0.1805 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3435   -0.0241   -0.7199 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5760   -0.1308    0.1005 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2635   -1.4981   -0.5347 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1414   -1.2747    0.3284 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3157    0.1377    1.1755 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6427   -1.5835    1.2831 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8582   -1.0351   -1.5163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6727    1.4756   -0.4988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8151    0.9301   -1.9561 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7193    2.0238   -0.4505 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2682    0.8423    0.8897 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5391    0.1036   -1.7865 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4989   -0.7311    1.0064 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4247   -0.4760   -0.5609 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8840    0.9145    0.3953 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
  5  7  1  0
  7  2  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  6 17  1  0
  6 18  1  0
  6 19  1  0
M  END
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3D SDF for HMDB0302173 (2,5-Dimethyltetrahydrothiophene)


  Mrv1533007131513272D          

  7  7  0  0  0  0            999 V2000
   -0.3297   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  5  3  1  0  0  0  0
  6  2  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  7  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0302173

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1CCC(C)S1

> <INCHI_IDENTIFIER>
InChI=1S/C6H12S/c1-5-3-4-6(2)7-5/h5-6H,3-4H2,1-2H3

> <INCHI_KEY>
IBKCTZVPGMUZGZ-UHFFFAOYSA-N

> <FORMULA>
C6H12S

> <MOLECULAR_WEIGHT>
116.22

> <EXACT_MASS>
116.06597156

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
13.892097382833095

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,5-dimethylthiolane

> <ALOGPS_LOGP>
2.87

> <JCHEM_LOGP>
2.047415160333333

> <ALOGPS_LOGS>
-2.69

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
35.4671

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.37e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,5-dimethylthiolane

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0302173 (2,5-Dimethyltetrahydrothiophene)

HMDB0302173
     RDKit          3D
2,5-Dimethyltetrahydrothiophene
 19 19  0  0  0  0  0  0  0  0999 V2000
   -2.1488   -0.8329    0.6375 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3555   -0.6334   -0.6079 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9350    0.7713   -0.8687 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3678    1.0207   -0.1805 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3435   -0.0241   -0.7199 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5760   -0.1308    0.1005 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2635   -1.4981   -0.5347 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1414   -1.2747    0.3284 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3157    0.1377    1.1755 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6427   -1.5835    1.2831 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8582   -1.0351   -1.5163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6727    1.4756   -0.4988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8151    0.9301   -1.9561 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7193    2.0238   -0.4505 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2682    0.8423    0.8897 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5391    0.1036   -1.7865 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4989   -0.7311    1.0064 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4247   -0.4760   -0.5609 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8840    0.9145    0.3953 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
  5  7  1  0
  7  2  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  6 17  1  0
  6 18  1  0
  6 19  1  0
M  END
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PDB for HMDB0302173 (2,5-Dimethyltetrahydrothiophene)

HEADER    PROTEIN                                 13-JUL-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-JUL-15         0                                  
HETATM    1  C   UNK     0      -0.615  -1.536   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    7  S   UNK     0      -0.186   1.175   0.000  0.00  0.00           S+0
CONECT    1    5                                                            
CONECT    2    6                                                            
CONECT    3    4    5                                                       
CONECT    4    3    6                                                       
CONECT    5    1    3    7                                                  
CONECT    6    2    4    7                                                  
CONECT    7    5    6                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0302173 (2,5-Dimethyltetrahydrothiophene)

COMPND    HMDB0302173
HETATM    1  C1  UNL     1      -2.149  -0.833   0.638  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.355  -0.633  -0.608  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.935   0.771  -0.869  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.368   1.021  -0.181  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.343  -0.024  -0.720  1.00  0.00           C  
HETATM    6  C6  UNL     1       2.576  -0.131   0.101  1.00  0.00           C  
HETATM    7  S1  UNL     1       0.263  -1.498  -0.535  1.00  0.00           S  
HETATM    8  H1  UNL     1      -3.141  -1.275   0.328  1.00  0.00           H  
HETATM    9  H2  UNL     1      -2.316   0.138   1.175  1.00  0.00           H  
HETATM   10  H3  UNL     1      -1.643  -1.584   1.283  1.00  0.00           H  
HETATM   11  H4  UNL     1      -1.858  -1.035  -1.516  1.00  0.00           H  
HETATM   12  H5  UNL     1      -1.673   1.476  -0.499  1.00  0.00           H  
HETATM   13  H6  UNL     1      -0.815   0.930  -1.956  1.00  0.00           H  
HETATM   14  H7  UNL     1       0.719   2.024  -0.451  1.00  0.00           H  
HETATM   15  H8  UNL     1       0.268   0.842   0.890  1.00  0.00           H  
HETATM   16  H9  UNL     1       1.539   0.104  -1.787  1.00  0.00           H  
HETATM   17  H10 UNL     1       2.499  -0.731   1.006  1.00  0.00           H  
HETATM   18  H11 UNL     1       3.425  -0.476  -0.561  1.00  0.00           H  
HETATM   19  H12 UNL     1       2.884   0.915   0.395  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    7   11
CONECT    3    4   12   13
CONECT    4    5   14   15
CONECT    5    6    7   16
CONECT    6   17   18   19
END
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SMILES for HMDB0302173 (2,5-Dimethyltetrahydrothiophene)

CC1CCC(C)S1
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INCHI for HMDB0302173 (2,5-Dimethyltetrahydrothiophene)

InChI=1S/C6H12S/c1-5-3-4-6(2)7-5/h5-6H,3-4H2,1-2H3
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC6H12S
Average Molecular Weight116.22
Monoisotopic Molecular Weight116.06597156
IUPAC Name2,5-dimethylthiolane
Traditional Name2,5-dimethylthiolane
CAS Registry NumberNot Available
SMILES
CC1CCC(C)S1
InChI Identifier
InChI=1S/C6H12S/c1-5-3-4-6(2)7-5/h5-6H,3-4H2,1-2H3
InChI KeyIBKCTZVPGMUZGZ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as thiolanes. These are organic compounds containing thiolane, a five-member saturated ring containing four carbon atoms and a sulfur atom.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassThiolanes
Sub ClassNot Available
Direct ParentThiolanes
Alternative Parents
Substituents
  • Thiolane
  • Dialkylthioether
  • Thioether
  • 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
logP2.87ALOGPS
logP2.05ChemAxon
logS-2.7ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity35.47 m³·mol⁻¹ChemAxon
Polarizability13.89 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]+122.53932859911
AllCCS[M+H-H2O]+117.77532859911
AllCCS[M+Na]+128.27132859911
AllCCS[M+NH4]+126.98732859911
AllCCS[M-H]-132.68632859911
AllCCS[M+Na-2H]-135.86832859911
AllCCS[M+HCOO]-139.432859911
DeepCCS[M+H]+133.9630932474
DeepCCS[M-H]-131.9230932474
DeepCCS[M-2H]-167.73630932474
DeepCCS[M+Na]+142.46330932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethyltetrahydrothiophene 10V, Positive-QTOFsplash10-014i-0900000000-54d3f6aa3591ae0d91952016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethyltetrahydrothiophene 20V, Positive-QTOFsplash10-014i-2900000000-4bbb19b6de3c73bfff242016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethyltetrahydrothiophene 40V, Positive-QTOFsplash10-06r6-9000000000-053d84c21a484c7bc1442016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethyltetrahydrothiophene 10V, Negative-QTOFsplash10-014i-9600000000-87eb06a4b11401ad889e2016-08-04Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethyltetrahydrothiophene 20V, Negative-QTOFsplash10-014i-8900000000-2c86c114e2a4875370472016-08-04Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethyltetrahydrothiophene 40V, Negative-QTOFsplash10-0a59-9000000000-2c6ccb188c7149454aa12016-08-04Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethyltetrahydrothiophene 10V, Positive-QTOFsplash10-067l-9400000000-ac584dd28a8a30fe62ab2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethyltetrahydrothiophene 20V, Positive-QTOFsplash10-0cdl-9200000000-3da47fa6ce6e9de63a1b2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethyltetrahydrothiophene 40V, Positive-QTOFsplash10-0a7i-9000000000-4e623559cb22235e33c62021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethyltetrahydrothiophene 10V, Negative-QTOFsplash10-014i-0900000000-32451cb42d50036ae1152021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethyltetrahydrothiophene 20V, Negative-QTOFsplash10-014i-0900000000-847b2987b90f35da11272021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,5-Dimethyltetrahydrothiophene 40V, Negative-QTOFsplash10-066r-7900000000-3027a915b83721a384ff2021-10-21Wishart 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 IDFDB003719
KNApSAcK IDNot Available
Chemspider ID14513
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound15247
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available