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Showing metabocard for xi-Tetrahydro-2-thiophenethiol (HMDB0040250)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 01:47:11 UTC
Update Date2023-02-21 17:28:02 UTC
HMDB IDHMDB0040250
Secondary Accession Numbers
  • HMDB40250
Metabolite Identification
Common Namexi-Tetrahydro-2-thiophenethiol
Descriptionxi-Tetrahydro-2-thiophenethiol 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. Based on a literature review very few articles have been published on xi-Tetrahydro-2-thiophenethiol.
Structure
Data?1677000482
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0040250 (xi-Tetrahydro-2-thiophenethiol)


  Mrv0541 02241211292D          

  6  6  0  0  0  0            999 V2000
    0.0226    0.6353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8024    0.6353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0582   -0.1498    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3912   -0.6353    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.2743   -0.1498    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0582   -0.4056    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
M  END
Download

3D MOL for HMDB0040250 (xi-Tetrahydro-2-thiophenethiol)

HMDB0040250
     RDKit          3D
xi-Tetrahydro-2-thiophenethiol
 14 14  0  0  0  0  0  0  0  0999 V2000
    2.6881   -0.0202   -0.6940 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.1563    0.0598    0.2255 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1063   -0.9094   -0.2737 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2245   -0.4112    0.2081 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4026    0.9914   -0.2900 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3106    1.6437   -0.1642 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.7190    0.5238    0.1304 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2713   -0.0674    1.3146 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1358   -1.0462   -1.3583 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3009   -1.8745    0.2407 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2370   -0.4422    1.3105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0041   -1.0364   -0.2306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7475    1.0659   -1.3209 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0725    1.5230    0.4125 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  2  1  0
  1  7  1  0
  2  8  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
M  END
Download

3D SDF for HMDB0040250 (xi-Tetrahydro-2-thiophenethiol)


  Mrv0541 02241211292D          

  6  6  0  0  0  0            999 V2000
    0.0226    0.6353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8024    0.6353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0582   -0.1498    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3912   -0.6353    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.2743   -0.1498    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0582   -0.4056    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0040250

> <DATABASE_NAME>
hmdb

> <SMILES>
SC1CCCS1

> <INCHI_IDENTIFIER>
InChI=1S/C4H8S2/c5-4-2-1-3-6-4/h4-5H,1-3H2

> <INCHI_KEY>
MBURDTXKYKCZEZ-UHFFFAOYSA-N

> <FORMULA>
C4H8S2

> <MOLECULAR_WEIGHT>
120.236

> <EXACT_MASS>
120.006741636

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
12.92842369669696

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
thiolane-2-thiol

> <ALOGPS_LOGP>
1.67

> <JCHEM_LOGP>
1.692226172

> <ALOGPS_LOGS>
-2.13

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.557885619740455

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
33.941

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.88e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thiolane-2-thiol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0040250 (xi-Tetrahydro-2-thiophenethiol)

HMDB0040250
     RDKit          3D
xi-Tetrahydro-2-thiophenethiol
 14 14  0  0  0  0  0  0  0  0999 V2000
    2.6881   -0.0202   -0.6940 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.1563    0.0598    0.2255 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1063   -0.9094   -0.2737 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2245   -0.4112    0.2081 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4026    0.9914   -0.2900 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3106    1.6437   -0.1642 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.7190    0.5238    0.1304 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2713   -0.0674    1.3146 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1358   -1.0462   -1.3583 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3009   -1.8745    0.2407 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2370   -0.4422    1.3105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0041   -1.0364   -0.2306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7475    1.0659   -1.3209 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0725    1.5230    0.4125 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  2  1  0
  1  7  1  0
  2  8  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
M  END
Download

PDB for HMDB0040250 (xi-Tetrahydro-2-thiophenethiol)

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       0.042   1.186   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.498   1.186   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.975  -0.280   0.000  0.00  0.00           C+0
HETATM    4  S   UNK     0      -0.730  -1.186   0.000  0.00  0.00           S+0
HETATM    5  C   UNK     0       0.512  -0.280   0.000  0.00  0.00           C+0
HETATM    6  S   UNK     0       1.975  -0.757   0.000  0.00  0.00           S+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    1    4    6                                                  
CONECT    6    5                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
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3D PDB for HMDB0040250 (xi-Tetrahydro-2-thiophenethiol)

COMPND    HMDB0040250
HETATM    1  S1  UNL     1       2.688  -0.020  -0.694  1.00  0.00           S  
HETATM    2  C1  UNL     1       1.156   0.060   0.226  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.106  -0.909  -0.274  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.225  -0.411   0.208  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.403   0.991  -0.290  1.00  0.00           C  
HETATM    6  S2  UNL     1       0.311   1.644  -0.164  1.00  0.00           S  
HETATM    7  H1  UNL     1       3.719   0.524   0.130  1.00  0.00           H  
HETATM    8  H2  UNL     1       1.271  -0.067   1.315  1.00  0.00           H  
HETATM    9  H3  UNL     1       0.136  -1.046  -1.358  1.00  0.00           H  
HETATM   10  H4  UNL     1       0.301  -1.875   0.241  1.00  0.00           H  
HETATM   11  H5  UNL     1      -1.237  -0.442   1.311  1.00  0.00           H  
HETATM   12  H6  UNL     1      -2.004  -1.036  -0.231  1.00  0.00           H  
HETATM   13  H7  UNL     1      -1.748   1.066  -1.321  1.00  0.00           H  
HETATM   14  H8  UNL     1      -2.072   1.523   0.412  1.00  0.00           H  
CONECT    1    2    7
CONECT    2    3    6    8
CONECT    3    4    9   10
CONECT    4    5   11   12
CONECT    5    6   13   14
END
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SMILES for HMDB0040250 (xi-Tetrahydro-2-thiophenethiol)

SC1CCCS1
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INCHI for HMDB0040250 (xi-Tetrahydro-2-thiophenethiol)

InChI=1S/C4H8S2/c5-4-2-1-3-6-4/h4-5H,1-3H2
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC4H8S2
Average Molecular Weight120.236
Monoisotopic Molecular Weight120.006741636
IUPAC Namethiolane-2-thiol
Traditional Namethiolane-2-thiol
CAS Registry NumberNot Available
SMILES
SC1CCCS1
InChI Identifier
InChI=1S/C4H8S2/c5-4-2-1-3-6-4/h4-5H,1-3H2
InChI KeyMBURDTXKYKCZEZ-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
  • Alkylthiol
  • Hydrocarbon derivative
  • Organosulfur compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
Role
Biological role
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
Water Solubility0.89 g/LALOGPS
logP1.67ALOGPS
logP1.69ChemAxon
logS-2.1ALOGPS
pKa (Strongest Acidic)9.56ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity33.94 m³·mol⁻¹ChemAxon
Polarizability12.93 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]+122.21931661259
DarkChem[M-H]-116.84731661259
DeepCCS[M+H]+128.18230932474
DeepCCS[M-H]-126.24530932474
DeepCCS[M-2H]-161.74830932474
DeepCCS[M+Na]+136.22630932474
AllCCS[M+H]+121.832859911
AllCCS[M+H-H2O]+117.032859911
AllCCS[M+NH4]+126.332859911
AllCCS[M+Na]+127.532859911
AllCCS[M-H]-132.732859911
AllCCS[M+Na-2H]-136.532859911
AllCCS[M+HCOO]-140.732859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.2.84 minutes32390414
Predicted by Siyang on May 30, 202214.6745 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.8 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid85.2 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1835.7 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid487.4 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid175.5 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid342.0 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid230.2 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid448.1 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 Acid570.1 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)489.0 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1018.8 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid333.5 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1065.4 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid364.0 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid336.5 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate596.8 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA511.5 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water168.4 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
xi-Tetrahydro-2-thiophenethiolSC1CCCS11610.6Standard polar33892256
xi-Tetrahydro-2-thiophenethiolSC1CCCS11012.3Standard non polar33892256
xi-Tetrahydro-2-thiophenethiolSC1CCCS11034.0Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
xi-Tetrahydro-2-thiophenethiol,1TMS,isomer #1C[Si](C)(C)SC1CCCS11270.7Semi standard non polar33892256
xi-Tetrahydro-2-thiophenethiol,1TMS,isomer #1C[Si](C)(C)SC1CCCS11257.5Standard non polar33892256
xi-Tetrahydro-2-thiophenethiol,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)SC1CCCS11512.3Semi standard non polar33892256
xi-Tetrahydro-2-thiophenethiol,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)SC1CCCS11498.9Standard non polar33892256
Spectra
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 IDFDB019967
KNApSAcK IDNot Available
Chemspider ID458727
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound526191
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 References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .