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Showing NP-Card for Dihydro-3(2H)-thiophenone (NP0046130)

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Record Information
Version2.0
Created at2022-03-17 19:48:58 UTC
Updated at2022-03-17 19:48:58 UTC
NP-MRD IDNP0046130
Secondary Accession NumbersNone
Natural Product Identification
Common NameDihydro-3(2H)-thiophenone
DescriptionDihydro-3(2H)-thiophenone, also known as tetrahydro-thiophen-3-one or 3-thiacyclopentanone, 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. Dihydro-3(2H)-thiophenone is an extremely weak basic (essentially neutral) compound (based on its pKa). Dihydro-3(2H)-thiophenone is a buttery, clam, and garlic tasting compound. Outside of the human body, Dihydro-3(2H)-thiophenone has been detected, but not quantified in, coffee and coffee products and nuts. This could make dihydro-3(2H)-thiophenone a potential biomarker for the consumption of these foods.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0046130 (Dihydro-3(2H)-thiophenone)


  Mrv0541 05061305492D          

  6  6  0  0  0  0            999 V2000
   -0.0997    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
    1.2352    0.6294    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
    0.9803   -0.1553    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  2  0  0  0  0
  6  2  1  0  0  0  0
  6  3  1  0  0  0  0
M  END
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3D MOL for NP0046130 (Dihydro-3(2H)-thiophenone)

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3D SDF for NP0046130 (Dihydro-3(2H)-thiophenone)

  Mrv0541 05061305492D          

  6  6  0  0  0  0            999 V2000
   -0.0997    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
    1.2352    0.6294    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
    0.9803   -0.1553    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  2  0  0  0  0
  6  2  1  0  0  0  0
  6  3  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0046130

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O=C1CCSC1

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

> <INCHI_KEY>
DSXFPRKPFJRPIB-UHFFFAOYSA-N

> <FORMULA>
C4H6OS

> <MOLECULAR_WEIGHT>
102.155

> <EXACT_MASS>
102.013935504

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
10.167928168478127

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
thiolan-3-one

> <ALOGPS_LOGP>
-0.10

> <JCHEM_LOGP>
0.5544182343333333

> <ALOGPS_LOGS>
-0.43

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.407404620587528

> <JCHEM_PKA_STRONGEST_BASIC>
-7.565177724731786

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
26.8645

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.84e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thiolan-3-one

> <JCHEM_VEBER_RULE>
1

$$$$

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3D-SDF for NP0046130 (Dihydro-3(2H)-thiophenone)
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PDB for NP0046130 (Dihydro-3(2H)-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      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.306   1.175   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       1.830  -0.290   0.000  0.00  0.00           S+0
CONECT    1    2    4                                                       
CONECT    2    1    6                                                       
CONECT    3    4    6                                                       
CONECT    4    1    3    5                                                  
CONECT    5    4                                                            
CONECT    6    2    3                                                       
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END

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3D PDB for NP0046130 (Dihydro-3(2H)-thiophenone)
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SMILES for NP0046130 (Dihydro-3(2H)-thiophenone)
O=C1CCSC1
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INCHI for NP0046130 (Dihydro-3(2H)-thiophenone)
InChI=1S/C4H6OS/c5-4-1-2-6-3-4/h1-3H2
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View in JSmol
Synonyms
ValueSource
3-oxo-2,3,4, 5-TetrahydrothiopheneHMDB
3-oxo-2,3,4,5-TetrahydrothiopheneHMDB
3-OxotetrahydrothiopheneHMDB
3-TetrahydrothiophenoneHMDB
3-ThiacyclopentanoneHMDB
3-ThiolanoneHMDB
3-ThiophanoneHMDB
4,5-Dihydro-3(2H)thiophenoneHMDB
Dihydro-3-(2H)-thiophenoneHMDB
Dihydro-3-(2H)-thiophenone (tetrahydrothiophen-3-one)HMDB
Dihydrothiophen-3(2H)-oneHMDB
FEMA 3266HMDB
Tetrahydro-thiophen-3-oneHMDB
Tetrahydrothiophen-3-oneHMDB
Tetrahydrothiophene-3-oneHMDB
Thiolan-3-oneHMDB
Chemical FormulaC4H6OS
Average Mass102.1550 Da
Monoisotopic Mass102.01394 Da
IUPAC Namethiolan-3-one
Traditional Namethiolan-3-one
CAS Registry Number1003-04-9
SMILES
O=C1CCSC1
InChI Identifier
InChI=1S/C4H6OS/c5-4-1-2-6-3-4/h1-3H2
InChI KeyDSXFPRKPFJRPIB-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Coffea arabica L.FooDB
    • Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Coffea canephoraFooDB
    • Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
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
    • 

  • Cyclic ketone
    • 

  • Ketone
    • 

  • Dialkylthioether
    • 

  • Thioether
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Carbonyl group
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-0.1ALOGPS
logP0.55ChemAxon
logS-0.43ALOGPS
pKa (Strongest Acidic)18.41ChemAxon
pKa (Strongest Basic)-7.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area17.07 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity26.86 m³·mol⁻¹ChemAxon
Polarizability10.17 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0031242  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB003269  
KNApSAcK IDNot Available
Chemspider ID55193  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound61252  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available