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Showing metabocard for Pentachlorobenzene (HMDB0256246)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 16:34:27 UTC
Update Date2021-09-26 23:11:45 UTC
HMDB IDHMDB0256246
Secondary Accession NumbersNone
Metabolite Identification
Common NamePentachlorobenzene
Descriptionpentachlorobenzene, also known as PCB or QCB, belongs to the class of organic compounds known as chlorobenzenes. Chlorobenzenes are compounds containing one or more chlorine atoms attached to a benzene moiety. Based on a literature review a significant number of articles have been published on pentachlorobenzene. This compound has been identified in human blood as reported by (PMID: 31557052 ). Pentachlorobenzene is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Pentachlorobenzene 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 HMDB0256246 (Pentachlorobenzene)


  Mrv0541 02241205472D          

 11 11  0  0  0  0            999 V2000
    2.1434    1.2375    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    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
    0.7145   -0.4125    0.0000 C   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
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 Cl  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    1.2375    0.0000 Cl  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
    0.7145    2.0625    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
  2 10  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
Download

3D MOL for HMDB0256246 (Pentachlorobenzene)

HMDB0256246
     RDKit          3D
Pentachlorobenzene
 12 12  0  0  0  0  0  0  0  0999 V2000
   -2.7602   -1.6229   -0.0100 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.2269   -0.7589   -0.0047 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0187   -1.4258   -0.0091 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1880   -0.7564   -0.0050 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7323   -1.6103   -0.0108 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.2098    0.6221    0.0038 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7351    1.5097    0.0093 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.0150    1.3193    0.0085 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0204    3.0829    0.0198 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.1769    0.6237    0.0042 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6939    1.5208    0.0101 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.0167   -2.5042   -0.0160 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
  4  5  1  0
  4  6  2  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  2  0
 10 11  1  0
 10  2  1  0
  3 12  1  0
M  END
Download

3D SDF for HMDB0256246 (Pentachlorobenzene)


  Mrv0541 02241205472D          

 11 11  0  0  0  0            999 V2000
    2.1434    1.2375    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    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
    0.7145   -0.4125    0.0000 C   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
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 Cl  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    1.2375    0.0000 Cl  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
    0.7145    2.0625    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
  2 10  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256246

> <DATABASE_NAME>
hmdb

> <SMILES>
ClC1=CC(Cl)=C(Cl)C(Cl)=C1Cl

> <INCHI_IDENTIFIER>
InChI=1S/C6HCl5/c7-2-1-3(8)5(10)6(11)4(2)9/h1H

> <INCHI_KEY>
CEOCDNVZRAIOQZ-UHFFFAOYSA-N

> <FORMULA>
C6HCl5

> <MOLECULAR_WEIGHT>
250.337

> <EXACT_MASS>
247.852088567

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
19.667981893458457

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,2,3,4,5-pentachlorobenzene

> <ALOGPS_LOGP>
5.22

> <JCHEM_LOGP>
4.993469197666667

> <ALOGPS_LOGS>
-5.43

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
50.08200000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.21e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pentachlorobenzene

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0256246 (Pentachlorobenzene)

HMDB0256246
     RDKit          3D
Pentachlorobenzene
 12 12  0  0  0  0  0  0  0  0999 V2000
   -2.7602   -1.6229   -0.0100 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.2269   -0.7589   -0.0047 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0187   -1.4258   -0.0091 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1880   -0.7564   -0.0050 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7323   -1.6103   -0.0108 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.2098    0.6221    0.0038 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7351    1.5097    0.0093 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.0150    1.3193    0.0085 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0204    3.0829    0.0198 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.1769    0.6237    0.0042 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6939    1.5208    0.0101 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.0167   -2.5042   -0.0160 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
  4  5  1  0
  4  6  2  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  2  0
 10 11  1  0
 10  2  1  0
  3 12  1  0
M  END
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PDB for HMDB0256246 (Pentachlorobenzene)

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 Cl   UNK     0       4.001   2.310   0.000  0.00  0.00          Cl+0
HETATM    2  C   UNK     0       2.667   1.540   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       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5 Cl   UNK     0       1.334  -2.310   0.000  0.00  0.00          Cl+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7 Cl   UNK     0      -1.334  -0.770   0.000  0.00  0.00          Cl+0
HETATM    8  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    9 Cl   UNK     0      -1.334   2.310   0.000  0.00  0.00          Cl+0
HETATM   10  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   11 Cl   UNK     0       1.334   3.850   0.000  0.00  0.00          Cl+0
CONECT    1    2                                                            
CONECT    2    1    3   10                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8    2   11                                                  
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END
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3D PDB for HMDB0256246 (Pentachlorobenzene)

COMPND    HMDB0256246
HETATM    1 CL1  UNL     1      -2.760  -1.623  -0.010  1.00  0.00          CL  
HETATM    2  C1  UNL     1      -1.227  -0.759  -0.005  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.019  -1.426  -0.009  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.188  -0.756  -0.005  1.00  0.00           C  
HETATM    5 CL2  UNL     1       2.732  -1.610  -0.011  1.00  0.00          CL  
HETATM    6  C4  UNL     1       1.210   0.622   0.004  1.00  0.00           C  
HETATM    7 CL3  UNL     1       2.735   1.510   0.009  1.00  0.00          CL  
HETATM    8  C5  UNL     1       0.015   1.319   0.008  1.00  0.00           C  
HETATM    9 CL4  UNL     1      -0.020   3.083   0.020  1.00  0.00          CL  
HETATM   10  C6  UNL     1      -1.177   0.624   0.004  1.00  0.00           C  
HETATM   11 CL5  UNL     1      -2.694   1.521   0.010  1.00  0.00          CL  
HETATM   12  H1  UNL     1       0.017  -2.504  -0.016  1.00  0.00           H  
CONECT    1    2
CONECT    2    3    3   10
CONECT    3    4   12
CONECT    4    5    6    6
CONECT    6    7    8
CONECT    8    9   10   10
CONECT   10   11
END
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SMILES for HMDB0256246 (Pentachlorobenzene)

ClC1=CC(Cl)=C(Cl)C(Cl)=C1Cl
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INCHI for HMDB0256246 (Pentachlorobenzene)

InChI=1S/C6HCl5/c7-2-1-3(8)5(10)6(11)4(2)9/h1H
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1,2,3,4,5-PENTACHLOROBENZENEChEBI
PCBChEBI
PentachlorbenzolChEBI
QCBChEBI
Chemical FormulaC6HCl5
Average Molecular Weight250.337
Monoisotopic Molecular Weight247.852088567
IUPAC Name1,2,3,4,5-pentachlorobenzene
Traditional Namepentachlorobenzene
CAS Registry NumberNot Available
SMILES
ClC1=CC(Cl)=C(Cl)C(Cl)=C1Cl
InChI Identifier
InChI=1S/C6HCl5/c7-2-1-3(8)5(10)6(11)4(2)9/h1H
InChI KeyCEOCDNVZRAIOQZ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as chlorobenzenes. Chlorobenzenes are compounds containing one or more chlorine atoms attached to a benzene moiety.
KingdomOrganic compounds
Super ClassBenzenoids
ClassBenzene and substituted derivatives
Sub ClassHalobenzenes
Direct ParentChlorobenzenes
Alternative Parents
Substituents
  • Chlorobenzene
  • Aryl halide
  • Aryl chloride
  • Hydrocarbon derivative
  • Organochloride
  • Organohalogen compound
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External Descriptors
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
logP5.22ALOGPS
logP4.99ChemAxon
logS-5.4ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity50.08 m³·mol⁻¹ChemAxon
Polarizability19.67 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
DeepCCS[M+H]+140.40730932474
DeepCCS[M-H]-137.65630932474
DeepCCS[M-2H]-173.86130932474
DeepCCS[M+Na]+149.39930932474
AllCCS[M+H]+138.032859911
AllCCS[M+H-H2O]+134.132859911
AllCCS[M+NH4]+141.732859911
AllCCS[M+Na]+142.732859911
AllCCS[M-H]-115.732859911
AllCCS[M+Na-2H]-116.632859911
AllCCS[M+HCOO]-117.732859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
PentachlorobenzeneClC1=CC(Cl)=C(Cl)C(Cl)=C1Cl2073.8Standard polar33892256
PentachlorobenzeneClC1=CC(Cl)=C(Cl)C(Cl)=C1Cl1505.6Standard non polar33892256
PentachlorobenzeneClC1=CC(Cl)=C(Cl)C(Cl)=C1Cl1524.8Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Pentachlorobenzene GC-MS (Non-derivatized) - 70eV, Positivesplash10-0f6t-0090000000-75d0cae33b7068fd984d2021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pentachlorobenzene 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 - Pentachlorobenzene 10V, Positive-QTOFsplash10-0002-0090000000-ab5dd4d720170545d8ed2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentachlorobenzene 20V, Positive-QTOFsplash10-0002-0090000000-ab5dd4d720170545d8ed2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentachlorobenzene 40V, Positive-QTOFsplash10-0002-0090000000-e662e17ce77d406605b82016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentachlorobenzene 10V, Negative-QTOFsplash10-0002-0090000000-bc13fc5e695697a1e57e2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentachlorobenzene 20V, Negative-QTOFsplash10-0002-0090000000-bc13fc5e695697a1e57e2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pentachlorobenzene 40V, Negative-QTOFsplash10-0002-0090000000-bc13fc5e695697a1e57e2016-08-03Wishart 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 ID21106570
KEGG Compound IDC18141
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPentachlorobenzene
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID47136
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 ]