Np mrd loader

Showing NP-Card for Pentachlorophenol (NP0002857)

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Record Information
Version1.0
Created at2020-11-23 19:42:08 UTC
Updated at2021-08-19 23:59:28 UTC
NP-MRD IDNP0002857
Secondary Accession NumbersNone
Natural Product Identification
Common NamePentachlorophenol
Provided ByBMRBBMRB logo
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. It was first documented in 2008 (PMID: 17984079). Based on a literature review a significant number of articles have been published on Pentachlorophenol (PMID: 34327555) (PMID: 34199613) (PMID: 34182284) (PMID: 34173948) (PMID: 34173006) (PMID: 34121527).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002857 (Pentachlorophenol)


     RDKit          2D

 13 13  0  0  0  0  0  0  0  0999 V2000
   -2.5295   -0.9820    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1121   -0.4910    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8286    0.9820    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9625    1.9640    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.5888    1.4730    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8722    2.9459    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.7226    0.4910    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1400    0.9820    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.4392   -0.9820    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5731   -1.9640    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.0218   -1.4730    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2617   -2.9459    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -3.6633   -0.0000    0.0000 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 MOL for NP0002857 (Pentachlorophenol)

NP0002857
     RDKit          3D

 13 13  0  0  0  0  0  0  0  0999 V2000
   -1.6217   -1.9932    0.1063 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7335   -0.9259    0.0477 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6248   -1.1534   -0.0695 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1622   -2.8299   -0.1394 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.5478   -0.1323   -0.1317 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2624   -0.4663   -0.2803 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.1320    1.1844   -0.0773 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2945    2.5114   -0.1550 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.2201    1.4254    0.0396 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8353    3.0552    0.1153 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.1407    0.3953    0.1015 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8640    0.6822    0.2501 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -2.6085   -1.7528    0.1926 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 NP0002857 (Pentachlorophenol)


     RDKit          2D

 13 13  0  0  0  0  0  0  0  0999 V2000
   -2.5295   -0.9820    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1121   -0.4910    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8286    0.9820    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9625    1.9640    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.5888    1.4730    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8722    2.9459    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.7226    0.4910    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1400    0.9820    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.4392   -0.9820    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5731   -1.9640    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.0218   -1.4730    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2617   -2.9459    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -3.6633   -0.0000    0.0000 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
> <DATABASE_ID>
NP0002857

> <DATABASE_NAME>
NP-MRD

> <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

$$$$
Download

3D-SDF for NP0002857 (Pentachlorophenol)

NP0002857
     RDKit          3D

 13 13  0  0  0  0  0  0  0  0999 V2000
   -1.6217   -1.9932    0.1063 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7335   -0.9259    0.0477 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6248   -1.1534   -0.0695 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1622   -2.8299   -0.1394 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.5478   -0.1323   -0.1317 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2624   -0.4663   -0.2803 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.1320    1.1844   -0.0773 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2945    2.5114   -0.1550 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.2201    1.4254    0.0396 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8353    3.0552    0.1153 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.1407    0.3953    0.1015 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8640    0.6822    0.2501 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -2.6085   -1.7528    0.1926 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 NP0002857 (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 NP0002857 (Pentachlorophenol)

COMPND    NP0002857
HETATM    1  O1  UNL     1      -1.622  -1.993   0.106  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.733  -0.926   0.048  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.625  -1.153  -0.069  1.00  0.00           C  
HETATM    4 CL1  UNL     1       1.162  -2.830  -0.139  1.00  0.00          CL  
HETATM    5  C3  UNL     1       1.548  -0.132  -0.132  1.00  0.00           C  
HETATM    6 CL2  UNL     1       3.262  -0.466  -0.280  1.00  0.00          CL  
HETATM    7  C4  UNL     1       1.132   1.184  -0.077  1.00  0.00           C  
HETATM    8 CL3  UNL     1       2.295   2.511  -0.155  1.00  0.00          CL  
HETATM    9  C5  UNL     1      -0.220   1.425   0.040  1.00  0.00           C  
HETATM   10 CL4  UNL     1      -0.835   3.055   0.115  1.00  0.00          CL  
HETATM   11  C6  UNL     1      -1.141   0.395   0.101  1.00  0.00           C  
HETATM   12 CL5  UNL     1      -2.864   0.682   0.250  1.00  0.00          CL  
HETATM   13  H1  UNL     1      -2.608  -1.753   0.193  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 NP0002857 (Pentachlorophenol)

OC1=C(Cl)C(Cl)=C(Cl)C(Cl)=C1Cl
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INCHI for NP0002857 (Pentachlorophenol)

InChI=1S/C6HCl5O/c7-1-2(8)4(10)6(12)5(11)3(1)9/h12H
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View in JSmol
Synonyms
ValueSource
2,3,4,5,6-PentachlorophenolChEBI
PCPChEBI
1-Hydroxy-2,3,4,5,6-pentachlorobenzeneHMDB
2, 3,4,5,6-PentachlorophenolHMDB
2,3,4,5,6-Pentachlorophenol (acd/name 4.0)HMDB
Chem-tolHMDB
ChlorophenHMDB
Dowicide 7HMDB
Dowicide gHMDB
DurotoxHMDB
FungifenHMDB
Glazd pentaHMDB
Grundier arbezolHMDB
LauxtolHMDB
Lauxtol aHMDB
LiropremHMDB
PCP (Pesticide)HMDB
PenchlorolHMDB
PentaHMDB
Penta-kilHMDB
Pentachloro-phenolHMDB
PentachlorophenateHMDB
Pentachlorophenol pureHMDB
PentaconHMDB
PentasolHMDB
PenwarHMDB
PeratoxHMDB
PermacideHMDB
PermagardHMDB
PermasanHMDB
PermatoxHMDB
PermiteHMDB
Phenol, pentachloro-, pureHMDB
Preventol pHMDB
SantobriteHMDB
SantophenHMDB
Santophen 20HMDB
SinituhoHMDB
Term-i-trolHMDB
Thompson'S wood fixHMDB
WeedoneHMDB
Sodium pentachlorophenateHMDB
Pentachlorophenate, sodiumHMDB
Chemical FormulaC6HCl5O
Average Mass266.3370 Da
Monoisotopic Mass263.84700 Da
IUPAC Namepentachlorophenol
Traditional Namepermite
CAS Registry NumberNot Available
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 500 MHz, ethanol, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, ethanol, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Species Where Detected
Species NameSourceReference
Sphingobium chlorophenolicumKNApSAcK Database
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 ParentsNot Available
SubstituentsNot Available
Molecular FrameworkAromatic homomonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility9.48 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP4.99ALOGPS
logP4.69ChemAxon
logS-4.3ALOGPS
pKa (Strongest Acidic)4.98ChemAxon
pKa (Strongest Basic)-8.5ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area20.23 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity52.06 m³·mol⁻¹ChemAxon
Polarizability20.51 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0041974
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB 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
Good Scents IDrw1012311
References
General References
  1. Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL: BioMagResBank. Nucleic Acids Res. 2008 Jan;36(Database issue):D402-8. doi: 10.1093/nar/gkm957. Epub 2007 Nov 4. [PubMed:17984079 ]
  2. Ammeri RW, Hidri Y, Hassen W, Mehri I, Khlifi N, Hassen A: Surfactant efficiency on pentachlorophenol-contaminated wastewater enhanced by Pseudomonas putida AJ 785569. Arch Microbiol. 2021 Jul 29. pii: 10.1007/s00203-021-02486-1. doi: 10.1007/s00203-021-02486-1. [PubMed:34327555 ]
  3. Zhu BZ, Tang M, Huang CH, Mao L: Detecting and Quantifying Polyhaloaromatic Environmental Pollutants by Chemiluminescence-Based Analytical Method. Molecules. 2021 Jun 2;26(11). pii: molecules26113365. doi: 10.3390/molecules26113365. [PubMed:34199613 ]
  4. Xu L, Zhang J, Barnie S, Zhang H, Liu F, Chen H: New insight into the adsorption mechanism of PCP by humic substances with different degrees of humification in the presence of Cr(VI). Chemosphere. 2021 Jun 22;284:131223. doi: 10.1016/j.chemosphere.2021.131223. [PubMed:34182284 ]
  5. Yang WJ, Wu HB, Zhang C, Zhong Q, Hu MJ, He JL, Li GA, Zhu ZY, Zhu JL, Zhao HH, Zhang HS, Huang F: Exposure to 2,4-dichlorophenol, 2,4,6-trichlorophenol, pentachlorophenol and risk of thyroid cancer: a case-control study in China. Environ Sci Pollut Res Int. 2021 Jun 26. pii: 10.1007/s11356-021-14898-z. doi: 10.1007/s11356-021-14898-z. [PubMed:34173948 ]
  6. Hassen W, Cherif H, Werhani R, Raddadi N, Neifar M, Hassen A, Cherif A: Exhaustion of pentachlorophenol in soil microcosms with three Pseudomonas species as detoxification agents. Arch Microbiol. 2021 Sep;203(7):4641-4651. doi: 10.1007/s00203-021-02451-y. Epub 2021 Jun 25. [PubMed:34173006 ]
  7. Ammeri RW, Hassen W, Hidri Y, Di Rauso Simeone G, Hassen A: Macrophyte and indigenous bacterial co-remediation process for pentachlorophenol removal from wastewater. Int J Phytoremediation. 2021 Jun 12:1-12. doi: 10.1080/15226514.2021.1933897. [PubMed:34121527 ]
  8. Yavari S, Courchesne F, Brisson J: Nutrient-assisted phytoremediation of wood preservative-contaminated technosols with co-planting of Salix interior and Festuca arundinacea. Environ Sci Pollut Res Int. 2021 Jun 8. pii: 10.1007/s11356-021-14076-1. doi: 10.1007/s11356-021-14076-1. [PubMed:34101122 ]
  9. Chen Y, Zhang J, Dong Y, Duan T, Zhou Y, Li W: Phenolic compounds in water, suspended particulate matter and sediment from Weihe River in Northwest China. Water Sci Technol. 2021 Apr;83(8):2012-2024. doi: 10.2166/wst.2021.119. [PubMed:33905369 ]