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Showing metabocard for Pentachlorophenol (HMDB0041974)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2012-09-13 11:51:03 UTC
Update Date2022-03-07 02:57:14 UTC
HMDB IDHMDB0041974
Secondary Accession Numbers
  • HMDB41974
Metabolite Identification
Common NamePentachlorophenol
DescriptionPentachlorophenol, also known as PCP or chlorophen, belongs to the class of organic compounds known as p-chlorophenols. These are chlorophenols carrying a iodine at the C4 position of the benzene ring. Pentachlorophenol exists in all living organisms, ranging from bacteria to humans. Pentachlorophenol is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Pentachlorophenol is formally rated as a possible carcinogen (by IARC 2B) and is also a potentially toxic compound. Based on a literature review a significant number of articles have been published on Pentachlorophenol.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0041974 (Pentachlorophenol)

  Mrv0541 09051417102D          

 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 O   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
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3D MOL for HMDB0041974 (Pentachlorophenol)

HMDB0041974
     RDKit          3D
Pentachlorophenol
 13 13  0  0  0  0  0  0  0  0999 V2000
   -0.9396   -2.3836    0.2736 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4261   -1.1042    0.1261 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2085    0.0306    0.0907 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9290   -0.1560    0.2392 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.6498    1.2864   -0.0584 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6755    2.7083   -0.0992 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.7133    1.4582   -0.1781 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4099    3.0653   -0.3675 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.5007    0.3261   -0.1433 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2422    0.5445   -0.2962 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.9340   -0.9270    0.0061 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9776   -2.3513    0.0458 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.9492   -2.4973    0.3612 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
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3D SDF for HMDB0041974 (Pentachlorophenol)

  Mrv0541 09051417102D          

 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 O   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>
HMDB0041974

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1=C(Cl)C(Cl)=C(Cl)C(Cl)=C1Cl

> <INCHI_IDENTIFIER>
InChI=1S/C6HCl5O/c7-1-2(8)4(10)6(12)5(11)3(1)9/h12H

> <INCHI_KEY>
IZUPBVBPLAPZRR-UHFFFAOYSA-N

> <FORMULA>
C6HCl5O

> <MOLECULAR_WEIGHT>
266.337

> <EXACT_MASS>
263.847003189

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
20.51287694429776

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pentachlorophenol

> <ALOGPS_LOGP>
4.99

> <JCHEM_LOGP>
4.689903876

> <ALOGPS_LOGS>
-4.32

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.982652364488855

> <JCHEM_PKA_STRONGEST_BASIC>
-8.45473357950942

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
52.0629

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.27e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
permite

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0041974 (Pentachlorophenol)

HMDB0041974
     RDKit          3D
Pentachlorophenol
 13 13  0  0  0  0  0  0  0  0999 V2000
   -0.9396   -2.3836    0.2736 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4261   -1.1042    0.1261 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2085    0.0306    0.0907 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9290   -0.1560    0.2392 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.6498    1.2864   -0.0584 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6755    2.7083   -0.0992 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.7133    1.4582   -0.1781 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4099    3.0653   -0.3675 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.5007    0.3261   -0.1433 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2422    0.5445   -0.2962 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.9340   -0.9270    0.0061 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9776   -2.3513    0.0458 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.9492   -2.4973    0.3612 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
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PDB for HMDB0041974 (Pentachlorophenol)

HEADER    PROTEIN                                 05-SEP-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-14         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  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+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 HMDB0041974 (Pentachlorophenol)

COMPND    HMDB0041974
HETATM    1  O1  UNL     1      -0.940  -2.384   0.274  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.426  -1.104   0.126  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.208   0.031   0.091  1.00  0.00           C  
HETATM    4 CL1  UNL     1      -2.929  -0.156   0.239  1.00  0.00          CL  
HETATM    5  C3  UNL     1      -0.650   1.286  -0.058  1.00  0.00           C  
HETATM    6 CL2  UNL     1      -1.676   2.708  -0.099  1.00  0.00          CL  
HETATM    7  C4  UNL     1       0.713   1.458  -0.178  1.00  0.00           C  
HETATM    8 CL3  UNL     1       1.410   3.065  -0.367  1.00  0.00          CL  
HETATM    9  C5  UNL     1       1.501   0.326  -0.143  1.00  0.00           C  
HETATM   10 CL4  UNL     1       3.242   0.545  -0.296  1.00  0.00          CL  
HETATM   11  C6  UNL     1       0.934  -0.927   0.006  1.00  0.00           C  
HETATM   12 CL5  UNL     1       1.978  -2.351   0.046  1.00  0.00          CL  
HETATM   13  H1  UNL     1      -1.949  -2.497   0.361  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 HMDB0041974 (Pentachlorophenol)

OC1=C(Cl)C(Cl)=C(Cl)C(Cl)=C1Cl
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INCHI for HMDB0041974 (Pentachlorophenol)

InChI=1S/C6HCl5O/c7-1-2(8)4(10)6(12)5(11)3(1)9/h12H
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View in JSmolView Stereo Labels
Synonyms
Chemical FormulaC6HCl5O
Average Molecular Weight266.337
Monoisotopic Molecular Weight263.847003189
IUPAC Namepentachlorophenol
Traditional Namepermite
CAS Registry Number87-86-5
SMILES
OC1=C(Cl)C(Cl)=C(Cl)C(Cl)=C1Cl
InChI Identifier
InChI=1S/C6HCl5O/c7-1-2(8)4(10)6(12)5(11)3(1)9/h12H
InChI KeyIZUPBVBPLAPZRR-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as p-chlorophenols. These are chlorophenols carrying a iodine at the C4 position of the benzene ring.
KingdomOrganic compounds
Super ClassBenzenoids
ClassPhenols
Sub ClassHalophenols
Direct ParentP-chlorophenols
Alternative Parents
Substituents
  • 4-chlorophenol
  • 2-chlorophenol
  • 3-chlorophenol
  • Halobenzene
  • Chlorobenzene
  • Monocyclic benzene moiety
  • Aryl halide
  • Aryl chloride
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organochloride
  • Organohalogen compound
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point174 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility0.014 mg/mL at 25 °CNot Available
LogP5.12Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
Biospecimen Locations
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected and Quantified0.000505 (0.000424-0.000637) umol/mmol creatinineAdult (>18 years old)Not SpecifiedNormal
    • National Health a...
 details
UrineDetected and Quantified0.000743 (0.000586-0.00114) umol/mmol creatinineChildren (1-13 years old)Not SpecifiedNormal
    • National Health a...
 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 IDC00007496
Chemspider ID967
KEGG Compound IDC02575
BioCyc IDPENTACHLOROPHENOL
BiGG IDNot Available
Wikipedia LinkPentachlorophenol
METLIN IDNot Available
PubChem Compound992
PDB IDPCI
ChEBI ID17642
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00029814
Good Scents IDrw1012311
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References