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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 16:43:12 UTC
Update Date2021-09-26 23:11:58 UTC
HMDB IDHMDB0256360
Secondary Accession NumbersNone
Metabolite Identification
Common NamePexidartinib
DescriptionPexidartinib, also known as CML-261 or PLX-3397, belongs to the class of organic compounds known as pyrrolopyridines. Pyrrolopyridines are compounds containing a pyrrolopyridine moiety, which consists of a pyrrole ring fused to a pyridine. Pyrrole is 5-membered ring consisting of four carbon atoms and one nitrogen atom. Pyridine is a 6-membered ring consisting of five carbon atoms and one nitrogen center. Based on a literature review a significant number of articles have been published on Pexidartinib. This compound has been identified in human blood as reported by (PMID: 31557052 ). Pexidartinib is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Pexidartinib 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
CML-261ChEBI
PexidartinibumChEBI
PLX-3397ChEBI
PLX3397ChEBI
TuralioChEBI
5-((5-chloro-1H-pyrrolo(2,3-b)Pyridin-3-yl)methyl)-N-((6-(trifluoromethyl)pyridin-3-yl)methyl)pyridin-2-amineMeSH
Chemical FormulaC20H15ClF3N5
Average Molecular Weight417.82
Monoisotopic Molecular Weight417.0968077
IUPAC Name5-({5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl}methyl)-N-{[6-(trifluoromethyl)pyridin-3-yl]methyl}pyridin-2-amine
Traditional Name5-({5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl}methyl)-N-{[6-(trifluoromethyl)pyridin-3-yl]methyl}pyridin-2-amine
CAS Registry NumberNot Available
SMILES
FC(F)(F)C1=CC=C(CNC2=NC=C(CC3=CNC4=NC=C(Cl)C=C34)C=C2)C=N1
InChI Identifier
InChI=1S/C20H15ClF3N5/c21-15-6-16-14(10-28-19(16)29-11-15)5-12-2-4-18(26-7-12)27-9-13-1-3-17(25-8-13)20(22,23)24/h1-4,6-8,10-11H,5,9H2,(H,26,27)(H,28,29)
InChI KeyJGWRKYUXBBNENE-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrrolopyridines. Pyrrolopyridines are compounds containing a pyrrolopyridine moiety, which consists of a pyrrole ring fused to a pyridine. Pyrrole is 5-membered ring consisting of four carbon atoms and one nitrogen atom. Pyridine is a 6-membered ring consisting of five carbon atoms and one nitrogen center.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyrrolopyridines
Sub ClassNot Available
Direct ParentPyrrolopyridines
Alternative Parents
Substituents
  • Pyrrolopyridine
  • Aminopyridine
  • Aryl chloride
  • Aryl halide
  • Pyridine
  • Substituted pyrrole
  • Imidolactam
  • Pyrrole
  • Heteroaromatic compound
  • Azacycle
  • Amine
  • Organonitrogen compound
  • Organofluoride
  • Organochloride
  • Organohalogen compound
  • Alkyl halide
  • Alkyl fluoride
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic 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
logP4.64ALOGPS
logP4.54ChemAxon
logS-5.1ALOGPS
pKa (Strongest Acidic)15.68ChemAxon
pKa (Strongest Basic)6.76ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area66.49 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity105.89 m³·mol⁻¹ChemAxon
Polarizability39.33 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M-2H]-222.3130932474
DeepCCS[M+Na]+197.53830932474
AllCCS[M+H]+195.932859911
AllCCS[M+H-H2O]+193.332859911
AllCCS[M+NH4]+198.332859911
AllCCS[M+Na]+199.032859911
AllCCS[M-H]-190.032859911
AllCCS[M+Na-2H]-189.532859911
AllCCS[M+HCOO]-189.132859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
PexidartinibFC(F)(F)C1=CC=C(CNC2=NC=C(CC3=CNC4=NC=C(Cl)C=C34)C=C2)C=N14039.6Standard polar33892256
PexidartinibFC(F)(F)C1=CC=C(CNC2=NC=C(CC3=CNC4=NC=C(Cl)C=C34)C=C2)C=N13173.0Standard non polar33892256
PexidartinibFC(F)(F)C1=CC=C(CNC2=NC=C(CC3=CNC4=NC=C(Cl)C=C34)C=C2)C=N13539.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Pexidartinib,1TMS,isomer #1C[Si](C)(C)N(CC1=CC=C(C(F)(F)F)N=C1)C1=CC=C(CC2=C[NH]C3=NC=C(Cl)C=C23)C=N13164.6Semi standard non polar33892256
Pexidartinib,1TMS,isomer #1C[Si](C)(C)N(CC1=CC=C(C(F)(F)F)N=C1)C1=CC=C(CC2=C[NH]C3=NC=C(Cl)C=C23)C=N13087.4Standard non polar33892256
Pexidartinib,1TMS,isomer #1C[Si](C)(C)N(CC1=CC=C(C(F)(F)F)N=C1)C1=CC=C(CC2=C[NH]C3=NC=C(Cl)C=C23)C=N13775.3Standard polar33892256
Pexidartinib,1TMS,isomer #2C[Si](C)(C)N1C=C(CC2=CC=C(NCC3=CC=C(C(F)(F)F)N=C3)N=C2)C2=CC(Cl)=CN=C213291.1Semi standard non polar33892256
Pexidartinib,1TMS,isomer #2C[Si](C)(C)N1C=C(CC2=CC=C(NCC3=CC=C(C(F)(F)F)N=C3)N=C2)C2=CC(Cl)=CN=C212992.8Standard non polar33892256
Pexidartinib,1TMS,isomer #2C[Si](C)(C)N1C=C(CC2=CC=C(NCC3=CC=C(C(F)(F)F)N=C3)N=C2)C2=CC(Cl)=CN=C214009.8Standard polar33892256
Pexidartinib,2TMS,isomer #1C[Si](C)(C)N(CC1=CC=C(C(F)(F)F)N=C1)C1=CC=C(CC2=CN([Si](C)(C)C)C3=NC=C(Cl)C=C23)C=N13164.3Semi standard non polar33892256
Pexidartinib,2TMS,isomer #1C[Si](C)(C)N(CC1=CC=C(C(F)(F)F)N=C1)C1=CC=C(CC2=CN([Si](C)(C)C)C3=NC=C(Cl)C=C23)C=N13056.7Standard non polar33892256
Pexidartinib,2TMS,isomer #1C[Si](C)(C)N(CC1=CC=C(C(F)(F)F)N=C1)C1=CC=C(CC2=CN([Si](C)(C)C)C3=NC=C(Cl)C=C23)C=N13586.6Standard polar33892256
Pexidartinib,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(CC1=CC=C(C(F)(F)F)N=C1)C1=CC=C(CC2=C[NH]C3=NC=C(Cl)C=C23)C=N13350.7Semi standard non polar33892256
Pexidartinib,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(CC1=CC=C(C(F)(F)F)N=C1)C1=CC=C(CC2=C[NH]C3=NC=C(Cl)C=C23)C=N13256.3Standard non polar33892256
Pexidartinib,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(CC1=CC=C(C(F)(F)F)N=C1)C1=CC=C(CC2=C[NH]C3=NC=C(Cl)C=C23)C=N13816.9Standard polar33892256
Pexidartinib,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)N1C=C(CC2=CC=C(NCC3=CC=C(C(F)(F)F)N=C3)N=C2)C2=CC(Cl)=CN=C213504.5Semi standard non polar33892256
Pexidartinib,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)N1C=C(CC2=CC=C(NCC3=CC=C(C(F)(F)F)N=C3)N=C2)C2=CC(Cl)=CN=C213173.0Standard non polar33892256
Pexidartinib,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)N1C=C(CC2=CC=C(NCC3=CC=C(C(F)(F)F)N=C3)N=C2)C2=CC(Cl)=CN=C214028.0Standard polar33892256
Pexidartinib,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(CC1=CC=C(C(F)(F)F)N=C1)C1=CC=C(CC2=CN([Si](C)(C)C(C)(C)C)C3=NC=C(Cl)C=C23)C=N13530.0Semi standard non polar33892256
Pexidartinib,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(CC1=CC=C(C(F)(F)F)N=C1)C1=CC=C(CC2=CN([Si](C)(C)C(C)(C)C)C3=NC=C(Cl)C=C23)C=N13378.8Standard non polar33892256
Pexidartinib,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(CC1=CC=C(C(F)(F)F)N=C1)C1=CC=C(CC2=CN([Si](C)(C)C(C)(C)C)C3=NC=C(Cl)C=C23)C=N13685.1Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Pexidartinib GC-MS (Non-derivatized) - 70eV, Positivesplash10-0i0u-0339200000-ead78bedccbca204d5652021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pexidartinib 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 - Pexidartinib 10V, Positive-QTOFsplash10-014i-0111900000-ebc59003a72159d98d302017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pexidartinib 20V, Positive-QTOFsplash10-014i-0965700000-b03096ad3bcbe82a17832017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pexidartinib 40V, Positive-QTOFsplash10-014i-1970000000-48ca9e7852e4ce0883232017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pexidartinib 10V, Negative-QTOFsplash10-014i-0101900000-634ee789fbfbfbca78262017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pexidartinib 20V, Negative-QTOFsplash10-014j-0926800000-ae8bd8765105f7300c1d2017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pexidartinib 40V, Negative-QTOFsplash10-0002-1930000000-6798bfaa3bedb8517e0d2017-07-26Wishart 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 IDDB12978
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID35308322
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPexidartinib
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID145373
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 ]