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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 22:30:00 UTC

Update Date

2021-09-26 22:53:53 UTC

HMDB ID

HMDB0245430

Secondary Accession Numbers

None

Metabolite Identification

Common Name

2,3,4,5,6-Pentachlorobiphenyl

Description

2,3,4,5,6-Pentachlorobiphenyl, also known as PCB 116, belongs to the class of organic compounds known as polychlorinated biphenyls. These are organic compounds containing at least two chlorine atoms attached to either benzene ring of the biphenyl moiety. 2,3,4,5,6-Pentachlorobiphenyl is formally rated as a carcinogen (by IARC 1) and is also a potentially toxic compound. Based on a literature review a significant number of articles have been published on 2,3,4,5,6-Pentachlorobiphenyl. This compound has been identified in human blood as reported by (PMID: 31557052 ). 2,3,4,5,6-pentachlorobiphenyl is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 2,3,4,5,6-Pentachlorobiphenyl 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

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv0541 02241204262D          

 17 18  0  0  0  0            999 V2000
    0.7145   -0.4125    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
    1.4289   -1.6500    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
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    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
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
  8 13  1  0  0  0  0
  7 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
  2 16  1  0  0  0  0
 16 17  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0245430

> <DATABASE_NAME>
hmdb

> <SMILES>
ClC1=C(Cl)C(Cl)=C(C(Cl)=C1Cl)C1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C12H5Cl5/c13-8-7(6-4-2-1-3-5-6)9(14)11(16)12(17)10(8)15/h1-5H

> <INCHI_KEY>
GGMPTLAAIUQMIE-UHFFFAOYSA-N

> <FORMULA>
C12H5Cl5

> <MOLECULAR_WEIGHT>
326.433

> <EXACT_MASS>
323.883388695

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
28.62980910160426

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,2,3,4,5-pentachloro-6-phenylbenzene

> <ALOGPS_LOGP>
6.79

> <JCHEM_LOGP>
6.640694559666667

> <ALOGPS_LOGS>
-7.58

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
75.21820000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.53e-06 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3,4,5,6-pentachlorobiphenyl

> <JCHEM_VEBER_RULE>
1

$$$$

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       1.334  -0.770   0.000  0.00  0.00          Cl+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  -3.080   0.000  0.00  0.00           C+0
HETATM    4 Cl   UNK     0       4.001  -2.310   0.000  0.00  0.00          Cl+0
HETATM    5  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    6 Cl   UNK     0       4.001  -5.390   0.000  0.00  0.00          Cl+0
HETATM    7  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   15 Cl   UNK     0      -1.334  -5.390   0.000  0.00  0.00          Cl+0
HETATM   16  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   17 Cl   UNK     0      -1.334  -2.310   0.000  0.00  0.00          Cl+0
CONECT    1    2                                                            
CONECT    2    1    3   16                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   14                                                  
CONECT    8    7    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    8                                                       
CONECT   14    7   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14    2   17                                                  
CONECT   17   16                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
PCB 116	ChEBI

Chemical Formula

C₁₂H₅Cl₅

Average Molecular Weight

326.433

Monoisotopic Molecular Weight

323.883388695

IUPAC Name

1,2,3,4,5-pentachloro-6-phenylbenzene

Traditional Name

2,3,4,5,6-pentachlorobiphenyl

CAS Registry Number

Not Available

SMILES

ClC1=C(Cl)C(Cl)=C(C(Cl)=C1Cl)C1=CC=CC=C1

InChI Identifier

InChI=1S/C12H5Cl5/c13-8-7(6-4-2-1-3-5-6)9(14)11(16)12(17)10(8)15/h1-5H

InChI Key

GGMPTLAAIUQMIE-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as polychlorinated biphenyls. These are organic compounds containing at least two chlorine atoms attached to either benzene ring of the biphenyl moiety.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Biphenyls and derivatives

Direct Parent

Polychlorinated biphenyls

Alternative Parents

Substituents

Polychlorinated biphenyl
Halobenzene
Chlorobenzene
Aryl halide
Aryl chloride
Hydrocarbon derivative
Organochloride
Organohalogen compound
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

pentachlorobenzenes (CHEBI:34219 )
pentachlorobiphenyl (CHEBI:34219 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Cellular substructure

Membrane (HMDB: HMDB0245430)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	6.79	ALOGPS
logP	6.64	ChemAxon
logS	-7.6	ALOGPS
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	0 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	75.22 m³·mol⁻¹	ChemAxon
Polarizability	28.63 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	162.675	30932474
DeepCCS	[M-H]-	160.317	30932474
DeepCCS	[M-2H]-	193.205	30932474
DeepCCS	[M+Na]+	168.768	30932474
AllCCS	[M+H]+	157.2	32859911
AllCCS	[M+H-H2O]+	153.7	32859911
AllCCS	[M+NH4]+	160.5	32859911
AllCCS	[M+Na]+	161.5	32859911
AllCCS	[M-H]-	126.6	32859911
AllCCS	[M+Na-2H]-	125.6	32859911
AllCCS	[M+HCOO]-	124.5	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2,3,4,5,6-Pentachlorobiphenyl	ClC1=C(Cl)C(Cl)=C(C(Cl)=C1Cl)C1=CC=CC=C1	3037.5	Standard polar	33892256
2,3,4,5,6-Pentachlorobiphenyl	ClC1=C(Cl)C(Cl)=C(C(Cl)=C1Cl)C1=CC=CC=C1	2112.8	Standard non polar	33892256
2,3,4,5,6-Pentachlorobiphenyl	ClC1=C(Cl)C(Cl)=C(C(Cl)=C1Cl)C1=CC=CC=C1	2129.6	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 2,3,4,5,6-Pentachlorobiphenyl GC-MS (Non-derivatized) - 70eV, Positive	splash10-004i-1019000000-bf04ec1e4f2e1b51be5c	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2,3,4,5,6-Pentachlorobiphenyl GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
MS	Mass Spectrum (Electron Ionization)	splash10-004i-3946000000-98fc2825c251ffd4019f	2014-09-20	Not Available	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3,4,5,6-Pentachlorobiphenyl 10V, Positive-QTOF	splash10-00di-0009000000-b3ea3dfd658a9f739f06	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3,4,5,6-Pentachlorobiphenyl 20V, Positive-QTOF	splash10-00di-0009000000-d2c73c7f5689d99e1348	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3,4,5,6-Pentachlorobiphenyl 40V, Positive-QTOF	splash10-00ds-2095000000-08f930bced42959fdbb9	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3,4,5,6-Pentachlorobiphenyl 10V, Negative-QTOF	splash10-00di-0009000000-2aff60d3a19acec11656	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3,4,5,6-Pentachlorobiphenyl 20V, Negative-QTOF	splash10-00di-0009000000-bb09f081d6165339c050	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3,4,5,6-Pentachlorobiphenyl 40V, Negative-QTOF	splash10-0079-0094000000-66b5d95771ca9992c5f3	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3,4,5,6-Pentachlorobiphenyl 10V, Positive-QTOF	splash10-00di-0009000000-47057e0cfa248ce6ed12	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3,4,5,6-Pentachlorobiphenyl 20V, Positive-QTOF	splash10-00di-0009000000-47057e0cfa248ce6ed12	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3,4,5,6-Pentachlorobiphenyl 40V, Positive-QTOF	splash10-00di-0009000000-47057e0cfa248ce6ed12	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3,4,5,6-Pentachlorobiphenyl 10V, Negative-QTOF	splash10-00di-0009000000-3882219cf7a9a544b0b1	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3,4,5,6-Pentachlorobiphenyl 20V, Negative-QTOF	splash10-00di-0009000000-3882219cf7a9a544b0b1	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3,4,5,6-Pentachlorobiphenyl 40V, Negative-QTOF	splash10-00di-0093000000-f472cc4c884d06c6204b	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

16415

KEGG Compound ID

C14366

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

17348

PDB ID

Not Available

ChEBI ID

34219

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

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 ]

Showing metabocard for 2,3,4,5,6-Pentachlorobiphenyl (HMDB0245430)

MOL for HMDB0245430 (2,3,4,5,6-Pentachlorobiphenyl)

3D MOL for HMDB0245430 (2,3,4,5,6-Pentachlorobiphenyl)

3D SDF for HMDB0245430 (2,3,4,5,6-Pentachlorobiphenyl)

3D-SDF for HMDB0245430 (2,3,4,5,6-Pentachlorobiphenyl)

PDB for HMDB0245430 (2,3,4,5,6-Pentachlorobiphenyl)

3D PDB for HMDB0245430 (2,3,4,5,6-Pentachlorobiphenyl)

SMILES for HMDB0245430 (2,3,4,5,6-Pentachlorobiphenyl)

INCHI for HMDB0245430 (2,3,4,5,6-Pentachlorobiphenyl)

Structure for HMDB0245430 (2,3,4,5,6-Pentachlorobiphenyl)

3D Structure for HMDB0245430 (2,3,4,5,6-Pentachlorobiphenyl)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra