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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
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
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
logP4.75ALOGPS
logP4.13ChemAxon
logS-4.2ALOGPS
pKa (Strongest Basic)-0.92ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area31.35 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity66.86 m³·mol⁻¹ChemAxon
Polarizability26.52 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+159.6230932474
DeepCCS[M-H]-157.26230932474
DeepCCS[M-2H]-190.14730932474
DeepCCS[M+Na]+165.71330932474
AllCCS[M+H]+154.232859911
AllCCS[M+H-H2O]+150.932859911
AllCCS[M+NH4]+157.232859911
AllCCS[M+Na]+158.032859911
AllCCS[M-H]-144.932859911
AllCCS[M+Na-2H]-145.132859911
AllCCS[M+HCOO]-145.532859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
PenclomedineCOC1=C(Cl)C(OC)=C(Cl)C(=N1)C(Cl)(Cl)Cl2407.4Standard polar33892256
PenclomedineCOC1=C(Cl)C(OC)=C(Cl)C(=N1)C(Cl)(Cl)Cl1841.1Standard non polar33892256
PenclomedineCOC1=C(Cl)C(OC)=C(Cl)C(=N1)C(Cl)(Cl)Cl1890.8Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Penclomedine GC-MS (Non-derivatized) - 70eV, Positivesplash10-000i-0193000000-51dbd1aca8d6f23054992017-08-28Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Penclomedine 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 - Penclomedine 10V, Positive-QTOFsplash10-00di-0009000000-a95615ac402da78c6bba2017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Penclomedine 20V, Positive-QTOFsplash10-00di-0009000000-a95615ac402da78c6bba2017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Penclomedine 40V, Positive-QTOFsplash10-006x-0193000000-802d6b5f49c2a9a496cb2017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Penclomedine 10V, Negative-QTOFsplash10-00di-0009000000-d04c703f3600fc4dc96e2017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Penclomedine 20V, Negative-QTOFsplash10-00di-0019000000-77f08a570091d34f44ad2017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Penclomedine 40V, Negative-QTOFsplash10-00dl-0097000000-1076ec9486e80db3aaad2017-07-26Wishart 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 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 ]