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Showing metabocard for Dihydro-2(3H)-thiophenone (HMDB0031253)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-09-11 17:41:55 UTC
Update Date2023-02-21 17:20:12 UTC
HMDB IDHMDB0031253
Secondary Accession Numbers
  • HMDB31253
Metabolite Identification
Common NameDihydro-2(3H)-thiophenone
DescriptionDihydro-2(3H)-thiophenone, also known as 2-oxothiolane or 4-butyrothiolactone, 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 Dihydro-2(3H)-thiophenone.
Structure
Data?1677000012
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0031253 (Dihydro-2(3H)-thiophenone)


  Mrv0541 05061305502D          

  6  6  0  0  0  0            999 V2000
    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
    0.5678    1.9393    0.0000 O   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
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  4  2  0  0  0  0
  6  3  1  0  0  0  0
  6  4  1  0  0  0  0
M  END
Download

3D MOL for HMDB0031253 (Dihydro-2(3H)-thiophenone)

HMDB0031253
     RDKit          3D
Dihydro-2(3H)-thiophenone
 12 12  0  0  0  0  0  0  0  0999 V2000
    1.5434    2.2931   -0.2660 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7577    1.3906   -0.2531 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9173    0.1250    0.4767 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0493   -0.8720    0.0335 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3619   -0.2614   -0.3064 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8366    1.3014   -1.1073 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.9533   -0.2547    0.2303 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9152    0.2532    1.5816 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2716   -1.5168   -0.8242 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2422   -1.6028    0.8709 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9611    0.0512    0.5704 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9074   -0.9067   -1.0064 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  2  1  0
  3  7  1  0
  3  8  1  0
  4  9  1  0
  4 10  1  0
  5 11  1  0
  5 12  1  0
M  END
Download

3D SDF for HMDB0031253 (Dihydro-2(3H)-thiophenone)


  Mrv0541 05061305502D          

  6  6  0  0  0  0            999 V2000
    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
    0.5678    1.9393    0.0000 O   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
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  4  2  0  0  0  0
  6  3  1  0  0  0  0
  6  4  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0031253

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1CCCS1

> <INCHI_IDENTIFIER>
InChI=1S/C4H6OS/c5-4-2-1-3-6-4/h1-3H2

> <INCHI_KEY>
KMSNYNIWEORQDJ-UHFFFAOYSA-N

> <FORMULA>
C4H6OS

> <MOLECULAR_WEIGHT>
102.155

> <EXACT_MASS>
102.013935504

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
10.121710686655746

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
thiolan-2-one

> <ALOGPS_LOGP>
0.58

> <JCHEM_LOGP>
0.8004028483333332

> <ALOGPS_LOGS>
-0.42

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-6.053860639169298

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
26.653

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.90e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
gamma-thiobutyrolactone

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0031253 (Dihydro-2(3H)-thiophenone)

HMDB0031253
     RDKit          3D
Dihydro-2(3H)-thiophenone
 12 12  0  0  0  0  0  0  0  0999 V2000
    1.5434    2.2931   -0.2660 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7577    1.3906   -0.2531 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9173    0.1250    0.4767 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0493   -0.8720    0.0335 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3619   -0.2614   -0.3064 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8366    1.3014   -1.1073 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.9533   -0.2547    0.2303 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9152    0.2532    1.5816 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2716   -1.5168   -0.8242 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2422   -1.6028    0.8709 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9611    0.0512    0.5704 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9074   -0.9067   -1.0064 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  2  1  0
  3  7  1  0
  3  8  1  0
  4  9  1  0
  4 10  1  0
  5 11  1  0
  5 12  1  0
M  END
Download

PDB for HMDB0031253 (Dihydro-2(3H)-thiophenone)

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       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.060   3.620   0.000  0.00  0.00           O+0
HETATM    6  S   UNK     0      -0.186   1.175   0.000  0.00  0.00           S+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    6                                                       
CONECT    4    2    5    6                                                  
CONECT    5    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 HMDB0031253 (Dihydro-2(3H)-thiophenone)

COMPND    HMDB0031253
HETATM    1  O1  UNL     1       1.543   2.293  -0.266  1.00  0.00           O  
HETATM    2  C1  UNL     1       0.758   1.391  -0.253  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.917   0.125   0.477  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.049  -0.872   0.033  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.362  -0.261  -0.306  1.00  0.00           C  
HETATM    6  S1  UNL     1      -0.837   1.301  -1.107  1.00  0.00           S  
HETATM    7  H1  UNL     1       1.953  -0.255   0.230  1.00  0.00           H  
HETATM    8  H2  UNL     1       0.915   0.253   1.582  1.00  0.00           H  
HETATM    9  H3  UNL     1       0.272  -1.517  -0.824  1.00  0.00           H  
HETATM   10  H4  UNL     1      -0.242  -1.603   0.871  1.00  0.00           H  
HETATM   11  H5  UNL     1      -1.961   0.051   0.570  1.00  0.00           H  
HETATM   12  H6  UNL     1      -1.907  -0.907  -1.006  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    6
CONECT    3    4    7    8
CONECT    4    5    9   10
CONECT    5    6   11   12
END
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SMILES for HMDB0031253 (Dihydro-2(3H)-thiophenone)

O=C1CCCS1
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INCHI for HMDB0031253 (Dihydro-2(3H)-thiophenone)

InChI=1S/C4H6OS/c5-4-2-1-3-6-4/h1-3H2
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-OxothiolaneHMDB
2-ThiolanoneHMDB
4-ButyrothiolactoneHMDB
4-Mercaptobutanoic acid g-thiolactoneHMDB
4-ThiobutyrolactoneHMDB
Dihydro-2-(3H)-thiophenoneHMDB
g-ThiobutyrolactoneHMDB
gamma-ThiobutyrolactoneHMDB
Laquo gammaraquo -thiobutyrolactoneHMDB
Tetrahydro-2-thiophenoneHMDB
Thiacyclopentan-2-oneHMDB
Thiacyclopentanone-2HMDB
Thiolan-2-oneHMDB
Dihydro-2(3H)-thiophenoneMeSH
Chemical FormulaC4H6OS
Average Molecular Weight102.155
Monoisotopic Molecular Weight102.013935504
IUPAC Namethiolan-2-one
Traditional Namegamma-thiobutyrolactone
CAS Registry Number1003-10-7
SMILES
O=C1CCCS1
InChI Identifier
InChI=1S/C4H6OS/c5-4-2-1-3-6-4/h1-3H2
InChI KeyKMSNYNIWEORQDJ-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
  • Carbothioic s-lactone
  • Thiolane
  • Thiolactone
  • Thiocarboxylic acid ester
  • Thiocarboxylic acid or derivatives
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
RoleNot Available
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point195.00 to 197.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility35250 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP1.039 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility39 g/LALOGPS
logP0.58ALOGPS
logP0.8ChemAxon
logS-0.42ALOGPS
pKa (Strongest Basic)-6.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area17.07 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity26.65 m³·mol⁻¹ChemAxon
Polarizability10.12 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]+118.79831661259
DarkChem[M-H]-113.98731661259
DeepCCS[M+H]+126.92430932474
DeepCCS[M-H]-124.90730932474
DeepCCS[M-2H]-160.38430932474
DeepCCS[M+Na]+134.85730932474
AllCCS[M+H]+119.332859911
AllCCS[M+H-H2O]+114.332859911
AllCCS[M+NH4]+124.032859911
AllCCS[M+Na]+125.332859911
AllCCS[M-H]-125.532859911
AllCCS[M+Na-2H]-129.232859911
AllCCS[M+HCOO]-133.332859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Dihydro-2(3H)-thiophenoneO=C1CCCS11581.4Standard polar33892256
Dihydro-2(3H)-thiophenoneO=C1CCCS1912.9Standard non polar33892256
Dihydro-2(3H)-thiophenoneO=C1CCCS1994.3Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Dihydro-2(3H)-thiophenone GC-MS (Non-derivatized) - 70eV, Positivesplash10-0f96-9100000000-9ffb3adb72fd8cd8cde82017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Dihydro-2(3H)-thiophenone 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 - Dihydro-2(3H)-thiophenone 10V, Positive-QTOFsplash10-0udi-3900000000-89ef73bbab2f7cf8dbb12016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dihydro-2(3H)-thiophenone 20V, Positive-QTOFsplash10-0fe0-9300000000-092d07787455091f64922016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dihydro-2(3H)-thiophenone 40V, Positive-QTOFsplash10-0076-9000000000-687edfd25119594754672016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dihydro-2(3H)-thiophenone 10V, Negative-QTOFsplash10-0udi-1900000000-af6fa5af99969eaa2e922016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dihydro-2(3H)-thiophenone 20V, Negative-QTOFsplash10-0ue9-9400000000-cd583865fa7b586dd32b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dihydro-2(3H)-thiophenone 40V, Negative-QTOFsplash10-05ac-9000000000-e823911e195289b8f0e52016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dihydro-2(3H)-thiophenone 10V, Positive-QTOFsplash10-0udi-3900000000-67624d19ddc005f32e772021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dihydro-2(3H)-thiophenone 20V, Positive-QTOFsplash10-0ir3-9200000000-e3516f3ddc8ea1b945502021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dihydro-2(3H)-thiophenone 40V, Positive-QTOFsplash10-0f6x-9200000000-59deaff9a624150ebf8f2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dihydro-2(3H)-thiophenone 10V, Negative-QTOFsplash10-0udi-3900000000-e4590f196aa1e3ba70f12021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dihydro-2(3H)-thiophenone 20V, Negative-QTOFsplash10-0pc0-9200000000-49c43a090fb0acc262ee2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dihydro-2(3H)-thiophenone 40V, Negative-QTOFsplash10-001i-9100000000-a3aa3a701169fb99cb962021-09-22Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-16Wishart 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
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Clostridium difficile infection		 details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB003286
KNApSAcK IDNot Available
Chemspider ID13252
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound13852
PDB IDNot Available
ChEBI ID187055
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1248071
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.. .