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Showing metabocard for Pentachlorothiophenol (HMDB0256250)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 16:35:44 UTC
Update Date2021-09-26 23:11:46 UTC
HMDB IDHMDB0256250
Secondary Accession NumbersNone
Metabolite Identification
Common NamePentachlorothiophenol
Descriptionpentachlorobenzene-1-thiol belongs to the class of organic compounds known as thiophenols. Thiophenols are compounds containing a thiophenol ring, which a phenol derivative obtained by replacing the oxygen atom from the hydroxyl group (attached to the benzene) by a sulfur atom. Based on a literature review very few articles have been published on pentachlorobenzene-1-thiol. This compound has been identified in human blood as reported by (PMID: 31557052 ). Pentachlorothiophenol is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Pentachlorothiophenol is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0256250 (Pentachlorothiophenol)


  Mrv1572004191602502D          

 12 12  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    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    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
    2.1434    1.2375    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 Cl  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  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  2  0  0  0  0
  6  4  2  0  0  0  0
  6  5  1  0  0  0  0
  7  1  1  0  0  0  0
  8  2  1  0  0  0  0
  9  3  1  0  0  0  0
 10  4  1  0  0  0  0
 11  5  1  0  0  0  0
 12  6  1  0  0  0  0
M  END
Download

3D MOL for HMDB0256250 (Pentachlorothiophenol)

HMDB0256250
     RDKit          3D
Pentachlorothiophenol
 13 13  0  0  0  0  0  0  0  0999 V2000
    2.8345    0.4249   -0.6438 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.0864    0.1781   -0.4150 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5041   -1.0390   -0.2404 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5099   -2.4631   -0.2362 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.8532   -1.2076   -0.0648 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5558   -2.8108    0.1576 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.6617   -0.0860   -0.0661 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3769   -0.2773    0.1540 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.0929    1.1493   -0.2407 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1747    2.5407   -0.2330 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.2764    1.2919   -0.4155 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8962    2.9201   -0.6302 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    3.6076   -0.6213   -0.1679 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  5  7  2  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  2  0
 11 12  1  0
 11  2  1  0
  1 13  1  0
M  END
Download

3D SDF for HMDB0256250 (Pentachlorothiophenol)


  Mrv1572004191602502D          

 12 12  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    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    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
    2.1434    1.2375    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 Cl  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  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  2  0  0  0  0
  6  4  2  0  0  0  0
  6  5  1  0  0  0  0
  7  1  1  0  0  0  0
  8  2  1  0  0  0  0
  9  3  1  0  0  0  0
 10  4  1  0  0  0  0
 11  5  1  0  0  0  0
 12  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256250

> <DATABASE_NAME>
hmdb

> <SMILES>
SC1=C(Cl)C(Cl)=C(Cl)C(Cl)=C1Cl

> <INCHI_IDENTIFIER>
InChI=1S/C6HCl5S/c7-1-2(8)4(10)6(12)5(11)3(1)9/h12H

> <INCHI_KEY>
LLMLGZUZTFMXSA-UHFFFAOYSA-N

> <FORMULA>
C6HCl5S

> <MOLECULAR_WEIGHT>
282.38

> <EXACT_MASS>
279.8241597

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
22.597764018718614

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pentachlorobenzene-1-thiol

> <ALOGPS_LOGP>
5.49

> <JCHEM_LOGP>
5.086676377333333

> <ALOGPS_LOGS>
-5.33

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.8479412019342973

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
58.0918

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.33e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pentachlorothiophenol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0256250 (Pentachlorothiophenol)

HMDB0256250
     RDKit          3D
Pentachlorothiophenol
 13 13  0  0  0  0  0  0  0  0999 V2000
    2.8345    0.4249   -0.6438 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.0864    0.1781   -0.4150 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5041   -1.0390   -0.2404 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5099   -2.4631   -0.2362 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.8532   -1.2076   -0.0648 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5558   -2.8108    0.1576 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.6617   -0.0860   -0.0661 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3769   -0.2773    0.1540 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.0929    1.1493   -0.2407 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1747    2.5407   -0.2330 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.2764    1.2919   -0.4155 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8962    2.9201   -0.6302 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    3.6076   -0.6213   -0.1679 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  5  7  2  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  2  0
 11 12  1  0
 11  2  1  0
  1 13  1  0
M  END
Download

PDB for HMDB0256250 (Pentachlorothiophenol)

HEADER    PROTEIN                                 19-APR-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-16         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   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7 Cl   UNK     0       4.001   2.310   0.000  0.00  0.00          Cl+0
HETATM    8 Cl   UNK     0       1.334   3.850   0.000  0.00  0.00          Cl+0
HETATM    9 Cl   UNK     0       4.001  -0.770   0.000  0.00  0.00          Cl+0
HETATM   10 Cl   UNK     0      -1.334   2.310   0.000  0.00  0.00          Cl+0
HETATM   11 Cl   UNK     0       1.334  -2.310   0.000  0.00  0.00          Cl+0
HETATM   12  S   UNK     0      -1.334  -0.770   0.000  0.00  0.00           S+0
CONECT    1    2    3    7                                                  
CONECT    2    1    4    8                                                  
CONECT    3    1    5    9                                                  
CONECT    4    2    6   10                                                  
CONECT    5    3    6   11                                                  
CONECT    6    4    5   12                                                  
CONECT    7    1                                                            
CONECT    8    2                                                            
CONECT    9    3                                                            
CONECT   10    4                                                            
CONECT   11    5                                                            
CONECT   12    6                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END
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3D PDB for HMDB0256250 (Pentachlorothiophenol)

COMPND    HMDB0256250
HETATM    1  S1  UNL     1       2.835   0.425  -0.644  1.00  0.00           S  
HETATM    2  C1  UNL     1       1.086   0.178  -0.415  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.504  -1.039  -0.240  1.00  0.00           C  
HETATM    4 CL1  UNL     1       1.510  -2.463  -0.236  1.00  0.00          CL  
HETATM    5  C3  UNL     1      -0.853  -1.208  -0.065  1.00  0.00           C  
HETATM    6 CL2  UNL     1      -1.556  -2.811   0.158  1.00  0.00          CL  
HETATM    7  C4  UNL     1      -1.662  -0.086  -0.066  1.00  0.00           C  
HETATM    8 CL3  UNL     1      -3.377  -0.277   0.154  1.00  0.00          CL  
HETATM    9  C5  UNL     1      -1.093   1.149  -0.241  1.00  0.00           C  
HETATM   10 CL4  UNL     1      -2.175   2.541  -0.233  1.00  0.00          CL  
HETATM   11  C6  UNL     1       0.276   1.292  -0.415  1.00  0.00           C  
HETATM   12 CL5  UNL     1       0.896   2.920  -0.630  1.00  0.00          CL  
HETATM   13  H1  UNL     1       3.608  -0.621  -0.168  1.00  0.00           H  
CONECT    1    2   13
CONECT    2    3    3   11
CONECT    3    4    5
CONECT    5    6    7    7
CONECT    7    8    9
CONECT    9   10   11   11
CONECT   11   12
END
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SMILES for HMDB0256250 (Pentachlorothiophenol)

SC1=C(Cl)C(Cl)=C(Cl)C(Cl)=C1Cl
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INCHI for HMDB0256250 (Pentachlorothiophenol)

InChI=1S/C6HCl5S/c7-1-2(8)4(10)6(12)5(11)3(1)9/h12H
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View in JSmolView Stereo Labels
Synonyms
ValueSource
PentachlorothiophenolMeSH
Chemical FormulaC6HCl5S
Average Molecular Weight282.38
Monoisotopic Molecular Weight279.8241597
IUPAC Namepentachlorobenzene-1-thiol
Traditional Namepentachlorothiophenol
CAS Registry NumberNot Available
SMILES
SC1=C(Cl)C(Cl)=C(Cl)C(Cl)=C1Cl
InChI Identifier
InChI=1S/C6HCl5S/c7-1-2(8)4(10)6(12)5(11)3(1)9/h12H
InChI KeyLLMLGZUZTFMXSA-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as thiophenols. Thiophenols are compounds containing a thiophenol ring, which a phenol derivative obtained by replacing the oxygen atom from the hydroxyl group (attached to the benzene) by a sulfur atom.
KingdomOrganic compounds
Super ClassBenzenoids
ClassThiophenols
Sub ClassNot Available
Direct ParentThiophenols
Alternative Parents
Substituents
  • Thiophenol
  • Halobenzene
  • Chlorobenzene
  • Monocyclic benzene moiety
  • Aryl halide
  • Aryl chloride
  • Arylthiol
  • Hydrocarbon derivative
  • Organosulfur compound
  • Organochloride
  • Organohalogen compound
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological location
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
logP5.49ALOGPS
logP5.09ChemAxon
logS-5.3ALOGPS
pKa (Strongest Acidic)3.85ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity58.09 m³·mol⁻¹ChemAxon
Polarizability22.6 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+147.04230932474
DeepCCS[M-H]-144.68430932474
DeepCCS[M-2H]-179.84330932474
DeepCCS[M+Na]+155.38130932474
AllCCS[M+H]+140.332859911
AllCCS[M+H-H2O]+136.632859911
AllCCS[M+NH4]+143.732859911
AllCCS[M+Na]+144.732859911
AllCCS[M-H]-108.532859911
AllCCS[M+Na-2H]-108.932859911
AllCCS[M+HCOO]-109.332859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
PentachlorothiophenolSC1=C(Cl)C(Cl)=C(Cl)C(Cl)=C1Cl2620.3Standard polar33892256
PentachlorothiophenolSC1=C(Cl)C(Cl)=C(Cl)C(Cl)=C1Cl1764.7Standard non polar33892256
PentachlorothiophenolSC1=C(Cl)C(Cl)=C(Cl)C(Cl)=C1Cl1873.8Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Pentachlorothiophenol,1TMS,isomer #1C[Si](C)(C)SC1=C(Cl)C(Cl)=C(Cl)C(Cl)=C1Cl2040.8Semi standard non polar33892256
Pentachlorothiophenol,1TMS,isomer #1C[Si](C)(C)SC1=C(Cl)C(Cl)=C(Cl)C(Cl)=C1Cl2020.2Standard non polar33892256
Pentachlorothiophenol,1TMS,isomer #1C[Si](C)(C)SC1=C(Cl)C(Cl)=C(Cl)C(Cl)=C1Cl2053.0Standard polar33892256
Pentachlorothiophenol,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)SC1=C(Cl)C(Cl)=C(Cl)C(Cl)=C1Cl2347.1Semi standard non polar33892256
Pentachlorothiophenol,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)SC1=C(Cl)C(Cl)=C(Cl)C(Cl)=C1Cl2270.2Standard non polar33892256
Pentachlorothiophenol,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)SC1=C(Cl)C(Cl)=C(Cl)C(Cl)=C1Cl2209.8Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Pentachlorothiophenol GC-MS (Non-derivatized) - 70eV, Positivesplash10-001i-0190000000-da43c857a105370239922021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pentachlorothiophenol 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 - Pentachlorothiophenol 10V, Positive-QTOFsplash10-001i-0090000000-49b47be212654bdb1bd22016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentachlorothiophenol 20V, Positive-QTOFsplash10-001i-0090000000-49b47be212654bdb1bd22016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentachlorothiophenol 40V, Positive-QTOFsplash10-001l-0090000000-7bfdc1dfbc44279d6a712016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentachlorothiophenol 10V, Negative-QTOFsplash10-004i-0090000000-1faad83ab707aeed94ef2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentachlorothiophenol 20V, Negative-QTOFsplash10-004i-0090000000-36e6e8f6d328ad509b342016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentachlorothiophenol 40V, Negative-QTOFsplash10-004i-0090000000-1faad83ab707aeed94ef2016-08-03Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID8301
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
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. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]