Hmdb loader

Showing metabocard for Penclomedine (HMDB0256218)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Show more...Show more...Show more...
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 16:32:36 UTC
Update Date2021-09-26 23:11:43 UTC
HMDB IDHMDB0256218
Secondary Accession NumbersNone
Metabolite Identification
Common NamePenclomedine
DescriptionPenclomedine belongs to the class of organic compounds known as polyhalopyridines. These are organic compounds containing a pyridine ring substituted at two or more positions by a halogen atom. Based on a literature review very few articles have been published on Penclomedine. This compound has been identified in human blood as reported by (PMID: 31557052 ). Penclomedine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Penclomedine 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
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0256218 (Penclomedine)

  Mrv1652310211603482D          

 16 16  0  0  0  0            999 V2000
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   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    0.8250    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 N   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
    0.0000    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   -0.4125    0.0000 O   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
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.8250    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.7309   -1.1270    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.5559    0.3020    0.0000 Cl  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  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  3  8  1  0  0  0  0
  8  9  1  0  0  0  0
  7 10  1  0  0  0  0
 10 11  1  0  0  0  0
  5 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 12 15  1  0  0  0  0
  4 16  1  0  0  0  0
M  END
Download

3D MOL for HMDB0256218 (Penclomedine)

HMDB0256218
     RDKit          3D
Penclomedine
 22 22  0  0  0  0  0  0  0  0999 V2000
   -2.3151    2.8939   -0.2953 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9923    2.4921   -0.6789 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5803    1.1912   -0.4424 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3507    0.2459    0.1380 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9308   -1.0022    0.3555 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8191   -2.0009    0.9972 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3802   -1.2419    1.3638 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -2.0158   -3.4176   -0.0599 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.9951   -2.4983    2.5173 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.3374   -1.3854   -0.0129 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8940   -3.0361    0.2743 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.1618   -0.4479   -0.6116 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4476   -0.8227   -0.9893 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5475   -0.6999   -0.1215 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6969    0.8386   -0.8236 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7452    2.0402   -1.5878 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -2.5098    3.9368   -0.5364 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0661    2.1832   -0.6941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3783    2.8094    0.8265 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3711   -0.0953   -0.5467 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2358   -0.2377    0.8163 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8963   -1.7453    0.1115 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  6  9  1  0
  5 10  2  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 13 14  1  0
 12 15  2  0
 15 16  1  0
 15  3  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
 14 20  1  0
 14 21  1  0
 14 22  1  0
M  END
Download

3D SDF for HMDB0256218 (Penclomedine)

  Mrv1652310211603482D          

 16 16  0  0  0  0            999 V2000
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   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    0.8250    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 N   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
    0.0000    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   -0.4125    0.0000 O   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
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.8250    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.7309   -1.1270    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.5559    0.3020    0.0000 Cl  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  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  3  8  1  0  0  0  0
  8  9  1  0  0  0  0
  7 10  1  0  0  0  0
 10 11  1  0  0  0  0
  5 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 12 15  1  0  0  0  0
  4 16  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256218

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=C(Cl)C(OC)=C(Cl)C(=N1)C(Cl)(Cl)Cl

> <INCHI_IDENTIFIER>
InChI=1S/C8H6Cl5NO2/c1-15-5-3(9)6(8(11,12)13)14-7(16-2)4(5)10/h1-2H3

> <INCHI_KEY>
DZVPGIORVGSQMC-UHFFFAOYSA-N

> <FORMULA>
C8H6Cl5NO2

> <MOLECULAR_WEIGHT>
325.39

> <EXACT_MASS>
322.8841169

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
26.524500254242298

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3,5-dichloro-2,4-dimethoxy-6-(trichloromethyl)pyridine

> <ALOGPS_LOGP>
4.75

> <JCHEM_LOGP>
4.126536334666666

> <ALOGPS_LOGS>
-4.18

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-0.9204505207085422

> <JCHEM_POLAR_SURFACE_AREA>
31.35

> <JCHEM_REFRACTIVITY>
66.85669999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.17e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
penclomedine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0256218 (Penclomedine)

HMDB0256218
     RDKit          3D
Penclomedine
 22 22  0  0  0  0  0  0  0  0999 V2000
   -2.3151    2.8939   -0.2953 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9923    2.4921   -0.6789 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5803    1.1912   -0.4424 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3507    0.2459    0.1380 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9308   -1.0022    0.3555 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8191   -2.0009    0.9972 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3802   -1.2419    1.3638 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -2.0158   -3.4176   -0.0599 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.9951   -2.4983    2.5173 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.3374   -1.3854   -0.0129 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8940   -3.0361    0.2743 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.1618   -0.4479   -0.6116 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4476   -0.8227   -0.9893 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5475   -0.6999   -0.1215 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6969    0.8386   -0.8236 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7452    2.0402   -1.5878 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -2.5098    3.9368   -0.5364 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0661    2.1832   -0.6941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3783    2.8094    0.8265 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3711   -0.0953   -0.5467 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2358   -0.2377    0.8163 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8963   -1.7453    0.1115 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  6  9  1  0
  5 10  2  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 13 14  1  0
 12 15  2  0
 15 16  1  0
 15  3  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
 14 20  1  0
 14 21  1  0
 14 22  1  0
M  END
Download

PDB for HMDB0256218 (Penclomedine)

HEADER    PROTEIN                                 21-OCT-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   21-OCT-16         0                                  
HETATM    1  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       1.334  -0.770   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+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  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   13 Cl   UNK     0       5.335  -1.540   0.000  0.00  0.00          Cl+0
HETATM   14 Cl   UNK     0       3.231  -2.104   0.000  0.00  0.00          Cl+0
HETATM   15 Cl   UNK     0       4.771   0.564   0.000  0.00  0.00          Cl+0
HETATM   16 Cl   UNK     0       4.001   2.310   0.000  0.00  0.00          Cl+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5   16                                                  
CONECT    5    4    6   12                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   10                                                  
CONECT    8    7    3    9                                                  
CONECT    9    8                                                            
CONECT   10    7   11                                                       
CONECT   11   10                                                            
CONECT   12    5   13   14   15                                             
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15   12                                                            
CONECT   16    4                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END
Download

3D PDB for HMDB0256218 (Penclomedine)

COMPND    HMDB0256218
HETATM    1  C1  UNL     1      -2.315   2.894  -0.295  1.00  0.00           C  
HETATM    2  O1  UNL     1      -0.992   2.492  -0.679  1.00  0.00           O  
HETATM    3  C2  UNL     1      -0.580   1.191  -0.442  1.00  0.00           C  
HETATM    4  N1  UNL     1      -1.351   0.246   0.138  1.00  0.00           N  
HETATM    5  C3  UNL     1      -0.931  -1.002   0.356  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.819  -2.001   0.997  1.00  0.00           C  
HETATM    7 CL1  UNL     1      -3.380  -1.242   1.364  1.00  0.00          CL  
HETATM    8 CL2  UNL     1      -2.016  -3.418  -0.060  1.00  0.00          CL  
HETATM    9 CL3  UNL     1      -0.995  -2.498   2.517  1.00  0.00          CL  
HETATM   10  C5  UNL     1       0.337  -1.385  -0.013  1.00  0.00           C  
HETATM   11 CL4  UNL     1       0.894  -3.036   0.274  1.00  0.00          CL  
HETATM   12  C6  UNL     1       1.162  -0.448  -0.612  1.00  0.00           C  
HETATM   13  O2  UNL     1       2.448  -0.823  -0.989  1.00  0.00           O  
HETATM   14  C7  UNL     1       3.548  -0.700  -0.122  1.00  0.00           C  
HETATM   15  C8  UNL     1       0.697   0.839  -0.824  1.00  0.00           C  
HETATM   16 CL5  UNL     1       1.745   2.040  -1.588  1.00  0.00          CL  
HETATM   17  H1  UNL     1      -2.510   3.937  -0.536  1.00  0.00           H  
HETATM   18  H2  UNL     1      -3.066   2.183  -0.694  1.00  0.00           H  
HETATM   19  H3  UNL     1      -2.378   2.809   0.827  1.00  0.00           H  
HETATM   20  H4  UNL     1       4.371  -0.095  -0.547  1.00  0.00           H  
HETATM   21  H5  UNL     1       3.236  -0.238   0.816  1.00  0.00           H  
HETATM   22  H6  UNL     1       3.896  -1.745   0.112  1.00  0.00           H  
CONECT    1    2   17   18   19
CONECT    2    3
CONECT    3    4    4   15
CONECT    4    5
CONECT    5    6   10   10
CONECT    6    7    8    9
CONECT   10   11   12
CONECT   12   13   15   15
CONECT   13   14
CONECT   14   20   21   22
CONECT   15   16
END
Download

SMILES for HMDB0256218 (Penclomedine)

COC1=C(Cl)C(OC)=C(Cl)C(=N1)C(Cl)(Cl)Cl
Download

INCHI for HMDB0256218 (Penclomedine)

InChI=1S/C8H6Cl5NO2/c1-15-5-3(9)6(8(11,12)13)14-7(16-2)4(5)10/h1-2H3
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
3,5-dichloro-2,4-Dimethoxy-6-trichloromethylpyridineMeSH
Chemical FormulaC8H6Cl5NO2
Average Molecular Weight325.39
Monoisotopic Molecular Weight322.8841169
IUPAC Name3,5-dichloro-2,4-dimethoxy-6-(trichloromethyl)pyridine
Traditional Namepenclomedine
CAS Registry NumberNot Available
SMILES
COC1=C(Cl)C(OC)=C(Cl)C(=N1)C(Cl)(Cl)Cl
InChI Identifier
InChI=1S/C8H6Cl5NO2/c1-15-5-3(9)6(8(11,12)13)14-7(16-2)4(5)10/h1-2H3
InChI KeyDZVPGIORVGSQMC-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as polyhalopyridines. These are organic compounds containing a pyridine ring substituted at two or more positions by a halogen atom.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassHalopyridines
Direct ParentPolyhalopyridines
Alternative Parents
Substituents
  • Polyhalopyridine
  • Alkyl aryl ether
  • Aryl chloride
  • Aryl halide
  • Heteroaromatic compound
  • Azacycle
  • Ether
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organochloride
  • Organohalogen compound
  • Organopnictogen compound
  • Organic oxygen compound
  • Alkyl halide
  • Alkyl chloride
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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
Predicted Chromatographic Properties
Spectra
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 IDDB12987
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID54283
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 ]