Pexidartinib

drug
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Also known as CML-261Plx-3397PLX3397PEXIDARTINIBPLX-3397PEXIDARTINIB (PLX3397)

Summary

Pexidartinib (CHEMBL3813873) is an approved small-molecule EC 2.7.10.1 (receptor protein-tyrosine kinase) inhibitor (ATC L01EX15) targeting KIT, CSF1R, and FLT3; indicated across 16 conditions including neoplasm and tenosynovial giant cell tumor, diffuse type; with CIViC clinical evidence for 12 variant-indication associations (e.g. FLT3 F691L in acute myeloid leukemia).

At a glance

  • Status: Approved (max clinical phase 4)
  • Modality: Small molecule
  • ATC class: L01EX15
  • Targets: 8 (KIT, CSF1R, FLT3…)
  • Indications: 16 conditions
  • Clinical trials: 26
  • Precision-oncology evidence (CIViC): 12 variant–indication associations
  • Chemistry: 417.8 Da · C20H15ClF3N5

Identifiers

Drug identity and classification

FieldValue
ChEMBL IDCHEMBL3813873
NamePexidartinib
TypeSmall molecule
Max phase4
FDA approvedyes
PubChem CID25151352
ChEBICHEBI:145373
ATCL01EX15
Molecular formulaC20H15ClF3N5
Molecular weight417.8
InChIKeyJGWRKYUXBBNENE-UHFFFAOYSA-N

SMILES: C1=CC(=NC=C1CC2=CNC3=C2C=C(C=N3)Cl)NCC4=CN=C(C=C4)C(F)(F)F

IUPAC name: 5-[(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)methyl]-N-[[6-(trifluoromethyl)-3-pyridinyl]methyl]pyridin-2-amine

ChEBI definition: A pyrrolopyridine that is 5-chloro-1H-pyrrolo[2,3-b]pyridine which is substituted by a [6-({[6-(trifluoromethyl)pyridin-3-yl]methyl}amino)pyridin-3-yl]methyl group at position 3. It is a potent multi-targeted receptor tyrosine kinase inhibitor of CSF-1R, KIT, and FLT3 (IC50 of 20 nM, 10 nM and 160 nM, respectively). Approved by the FDA for the treatment of adult patients with symptomatic tenosynovial giant cell tumor (TGCT).

Pharmacological roles (ChEBI): EC 2.7.10.1 (receptor protein-tyrosine kinase) inhibitor, antineoplastic agent.

Also known as: CML-261, Pexidartinib, Plx-3397, PLX-3397, PLX3397, PEXIDARTINIB, PEXIDARTINIBPLX-3397, PEXIDARTINIB (PLX3397), pexidartinib

Parent form; salt/anhydrous children: CHEMBL3989973

Patent coverage: 1,475 distinct patent families (3,586 SureChEMBL compound mentions), from 3 matched compound structure(s). One matched structure accounts for 3,028 (84%) of the total. Mentions count patents naming the compound (not distinct inventions), so promiscuous / reference molecules inflate the mention figure — families are the dedup metric.

Targets

Targets

Primary targets (GtoPdb curated mechanism): the Cancer dependency column is the DepMap CRISPR fitness signal (% of screened cell lines dependent on the target).

GeneTargetActionpAffinityCancer dependencyUniProt
KITKIT proto-oncogene, receptor tyrosine kinaseInhibition7.570.5%P10721
CSF1Rcolony stimulating factor 1 receptorInhibition7.890%P07333
FLT3fms related receptor tyrosine kinase 3Inhibition6.80.9%P36888
FLT1fms related receptor tyrosine kinase 1Inhibition6.060.1%P17948
KDRkinase insert domain receptorInhibition6.361.1%P35968
NTRK3neurotrophic receptor tyrosine kinase 3Inhibition6.050%Q16288
CDK19cyclin dependent kinase 19Inhibition6.850.1%Q9BWU1
LCKLCK proto-oncogene, Src family tyrosine kinaseInhibition6.070.1%P06239

Broader ChEMBL bioactivity targets: 30 (assay-derived). Sample: Macrophage colony-stimulating factor 1 receptor, Alpha-2A adrenergic receptor, Vascular endothelial growth factor receptor 1, Platelet-derived growth factor receptor beta, Mast/stem cell growth factor receptor Kit, Receptor-type tyrosine-protein kinase FLT3, Platelet-derived growth factor receptor alpha, D(1A) dopamine receptor, Thromboxane A2 receptor, Progesterone receptor.

Bioactivity

ChEMBL activities: 104 potent at pChembl ≥ 5 of 110 total. Top 30 by potency (10 = 0.1 nM, 6 = 1 µM):

TargetpChemblTypeValueUnitActivity ID
CSF1R8.77IC501.7nMCHEMBL_ACT_24693942
CSF1R8.77IC501.7nMCHEMBL_ACT_24694186
CSF1R8.66IC502.2nMCHEMBL_ACT_29025737
CSF1R8.33IC504.7nMCHEMBL_ACT_25922565
FLT38.3IC505nMCHEMBL_ACT_16609130
CSF1R8.3IC505nMCHEMBL_ACT_25536023
CSF1R8.25IC505.61nMCHEMBL_ACT_25585245
CSF1R8.24Kd5.8nMCHEMBL_ACT_25465441
CSF1R8.24Kd5.8nMCHEMBL_ACT_25535943
PRKCQ8.22Kd6nMCHEMBL_ACT_17930841
KIT8.16IC506.9nMCHEMBL_ACT_29025740
FLT38.15IC507.1nMCHEMBL_ACT_24693962
FLT38.15IC507.1nMCHEMBL_ACT_24694211
FLT38.15IC507.1nMCHEMBL_ACT_29025746
FLT38.05IC509nMCHEMBL_ACT_26132408
PDGFRA8.02IC509.6nMCHEMBL_ACT_24693982
PDGFRA8.02IC509.6nMCHEMBL_ACT_24694236
PDGFRA8.02IC509.6nMCHEMBL_ACT_29025743
CSF1R8.01IC509.8nMCHEMBL_ACT_25465322
CSF1R8.01IC509.7nMCHEMBL_ACT_25535963
KIT8IC5010nMCHEMBL_ACT_25500506
KIT8IC5010nMCHEMBL_ACT_26186115
KIT8IC5010nMCHEMBL_ACT_26187727
KIT8IC5010nMCHEMBL_ACT_29055505
CSF1R7.97IC5010.8nMCHEMBL_ACT_18172205
FLT37.96IC5011nMCHEMBL_ACT_18893336
FLT37.96IC5011nMCHEMBL_ACT_24862906
FLT37.96IC5011nMCHEMBL_ACT_25016248
FLT37.96IC5011nMCHEMBL_ACT_25839758
CSF1R7.92IC5012nMCHEMBL_ACT_18930902

Target pathways

Aggregated over 8 target gene(s): KIT, CSF1R, FLT3, FLT1, KDR, NTRK3, CDK19, LCK.

Top Reactome pathways

124 total, by targets touching each:

PathwayTargetsGenes
PIP3 activates AKT signaling4FLT3, KIT, LCK, NTRK3
Constitutive Signaling by Aberrant PI3K in Cancer4FLT3, KIT, LCK, NTRK3
PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling4FLT3, KIT, LCK, NTRK3
Disease3CDK19, KIT, LCK
Developmental Biology2CDK19, KIT
Signaling by SCF-KIT2KIT, LCK
Regulation of KIT signaling2KIT, LCK
Signal Transduction2KIT, LCK
Neuropilin interactions with VEGF and VEGFR2FLT1, KDR
VEGF binds to VEGFR leading to receptor dimerization2FLT1, KDR
Negative regulation of the PI3K/AKT network2KIT, LCK
PI3K/AKT Signaling in Cancer2KIT, LCK
Diseases of signal transduction by growth factor receptors and second messengers2KIT, LCK
Infectious disease2CDK19, LCK
RAF/MAP kinase cascade2FLT3, KIT
Intracellular signaling by second messengers2KIT, LCK
Signaling by Receptor Tyrosine Kinases2KIT, LCK
FLT3 Signaling2FLT3, LCK
Signaling by KIT in disease2KIT, LCK
Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants2KIT, LCK
FLT3 signaling through SRC family kinases2FLT3, LCK
Viral Infection Pathways2CDK19, LCK
Hemostasis1LCK
PI3K Cascade1FLT3
GPVI-mediated activation cascade1LCK
Cytokine Signaling in Immune system1LCK
Adaptive Immune System1LCK
Metabolism1CDK19
HIV Infection1LCK
Host Interactions of HIV factors1LCK

Dominant GO biological processes

GO termTargets
protein phosphorylation8
cell surface receptor protein tyrosine kinase signaling pathway7
positive regulation of cell population proliferation6
positive regulation of MAPK cascade6
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction6
cell migration5
hemopoiesis5
positive regulation of cell migration5
protein autophosphorylation5
peptidyl-tyrosine phosphorylation5
regulation of cell shape3
cytokine-mediated signaling pathway3
regulation of cell population proliferation3
positive regulation of tyrosine phosphorylation of STAT protein3
positive regulation of gene expression3

Indications & clinical

Indications

16 indications (1 at ChEMBL trial phase 4). Phase below is the highest clinical-trial phase recorded for this drug against each disease — not the molecule’s overall approval status (that is in the Summary).

IndicationTrial phaseMONDOEFO
neoplasm4MONDO:0005070EFO:0000616
tenosynovial giant cell tumor, diffuse type3MONDO:0024686MONDO:0024686
glioblastoma2MONDO:0018177EFO:0000519
Hodgkins lymphoma2MONDO:0004952EFO:0000183
melanoma2MONDO:0005105EFO:0000756
metastatic melanoma2MONDO:0005191EFO:0002617
angiosarcoma2MONDO:0016982EFO:0003968
breast neoplasm2MONDO:0021100MONDO:0007254
rheumatoid arthritis1MONDO:0008383EFO:0000685
acute myeloid leukemia1MONDO:0018874EFO:0000222
prostate adenocarcinoma1MONDO:0005082EFO:0000673
malignant peripheral nerve sheath tumor1MONDO:0017827EFO:0000760
gastrointestinal stromal tumor1MONDO:0011719MONDO:0011719
liver disorder0MONDO:0005154EFO:0001421

2 further indication records had no mapped disease name (EFO/MeSH-only) or were duplicates, and are omitted.

Clinical trials

Total trials: 26.

Phase distribution

PhaseTrials
PHASE19
PHASE26
PHASE1/PHASE26
PHASE32
PHASE41
EARLY_PHASE11
Not specified1

Top trials by phase / activity

NCTPhaseStatusTitle
NCT04526704PHASE4COMPLETEDStudy to Evaluate Discontinuation and Re-Treatment in Participants With Tenosynovial Giant Cell Tumor (TGCT) Previously Treated With Pexidartinib
NCT04488822PHASE3ACTIVE_NOT_RECRUITINGA Study of the Efficacy and Safety of Pexidartinib in Adult Subjects With TGCT
NCT02371369PHASE3COMPLETEDPhase 3 Study of Pexidartinib for Pigmented Villonodular Synovitis (PVNS) or Giant Cell Tumor of the Tendon Sheath (GCT-TS)
NCT01042379PHASE2RECRUITINGI-SPY TRIAL: Neoadjuvant and Personalized Adaptive Novel Agents to Treat Breast Cancer
NCT04703322PHASE2ACTIVE_NOT_RECRUITINGA Study of Pexidartinib in Tenosynovial Giant Cell Tumor in Japan
NCT01217229PHASE2COMPLETEDSafety and Efficacy Study of PLX3397 in Adults With Relapsed or Refractory Hodgkin Lymphoma
NCT01349036PHASE2TERMINATEDA Phase 2 Study of PLX3397 in Patients With Recurrent Glioblastoma
NCT01349049PHASE1/PHASE2COMPLETEDPhase 1/2 Safety and Efficacy of PLX3397 in Adults With Relapsed or Refractory Acute Myeloid Leukemia (AML)
NCT01499043PHASE2TERMINATEDPilot Study of PLX3397 in Patients With Advanced Castration-Resistant Prostate Cancer (CRPC)
NCT01596751PHASE1/PHASE2COMPLETEDPhase Ib/II Study of PLX 3397 and Eribulin in Patients With Metastatic Breast Cancer
NCT01790503PHASE1/PHASE2COMPLETEDA Phase 1b/2 Study of PLX3397 + Radiation Therapy + Temozolomide in Patients With Newly Diagnosed Glioblastoma
NCT02071940PHASE2COMPLETEDPLX3397 KIT in Acral aNd mucOsal Melanoma
NCT02401815PHASE1/PHASE2COMPLETEDCGT9486 (Formerly Known as PLX9486) as a Single Agent and in Combination With PLX3397 (Pexidartinib) or Sunitinib in Participants With Advanced Solid Tumors
NCT02452424PHASE1/PHASE2TERMINATEDA Combination Clinical Study of PLX3397 and Pembrolizumab To Treat Advanced Melanoma and Other Solid Tumors
NCT02584647PHASE1/PHASE2TERMINATEDPLX3397 Plus Sirolimus in Unresectable Sarcoma and Malignant Peripheral Nerve Sheath Tumors
NCT01004861PHASE1COMPLETEDSafety Study of PLX108-01 in Patients With Solid Tumors
NCT01090570PHASE1WITHDRAWNSafety, Pharmacokinetic (PK), Pharmcodynamic (PD), and Drug-Drug Interaction of PLX3397 in Patients With Rheumatoid Arthritis Who Are Receiving Methotrexate
NCT01525602PHASE1COMPLETEDSafety Study of PLX3397 and Paclitaxel in Patients With Advanced Solid Tumors
NCT01826448PHASE1TERMINATEDA Phase 1b Open Label, Dose Escalation Study of PLX3397 in Combination With Vemurafenib in V600-mutated BRAF Melanoma
NCT02734433PHASE1COMPLETEDStudy of Pexidartinib in Asian Subjects With Advanced Solid Tumors
NCT02777710PHASE1COMPLETEDEvaluation of Safety and Activity of an Anti-PDL1 Antibody (DURVALUMAB) Combined With CSF-1R TKI (PEXIDARTINIB) in Patients With Metastatic/Advanced Pancreatic or Colorectal Cancers
NCT03138759PHASE1COMPLETEDEffect of Probenecid on Pexidartinib Pharmacokinetics
NCT03158103PHASE1COMPLETEDA Study of MEK162 (Binimetinib) in Combination With Pexidartinib in Patients With Advanced Gastrointestinal Stromal Tumor (GIST)
NCT03291288PHASE1COMPLETEDEffect of Pexidartinib on the Way the Body Processes CYP3A4 and CYP2C9 Substrates (Pharmacokinetics)
NCT04223635EARLY_PHASE1COMPLETEDStudy of Pexidartinib in Participants With Moderate Hepatic Impairment Compared With Healthy Participants
NCT02975700Not specifiedCOMPLETEDA Study of PLX3397 in Patients With Unresectable or Metastatic KIT-mutated Melanoma

Clinical evidence (CIViC)

Variant × indication × effect (12 predictive associations from 13 curated evidence items):

VariantIndicationEffectTherapyLevelCIViC
FLT3 F691LAcute Myeloid LeukemiaSensitivity/ResponsePexidartinibCIViC BEID8674 +1
CSF1 OverexpressionTenosynovial Giant Cell TumorSensitivity/ResponsePexidartinibCIViC BEID1969
FLT3 F691LAcute Myeloid LeukemiaResistancePexidartinibCIViC BEID9717
CSF1R ExpressionGlioblastomaSensitivity/ResponsePexidartinibCIViC DEID8132
CSF1R ExpressionGlioblastomaSensitivity/ResponseVatalanib + PexidartinibCIViC DEID8133
CSF1R ExpressionGlioblastomaSensitivity/ResponsePexidartinib + DovitinibCIViC DEID8134
FLT3 D839AAcute Myeloid LeukemiaResistancePexidartinibCIViC DEID8671
FLT3 D839HAcute Myeloid LeukemiaResistancePexidartinibCIViC DEID8673
FLT3 D839NAcute Myeloid LeukemiaResistancePexidartinibCIViC DEID8672
FLT3 ITD & D839GAcute Myeloid LeukemiaResistancePexidartinibCIViC DEID8669
FLT3 ITD & N841KAcute Myeloid LeukemiaResistancePexidartinibCIViC DEID9936
FLT3 M664IAcute Myeloid LeukemiaResistancePexidartinibCIViC DEID8667

Pharmacology

Pharmacogenomics

No CPIC/DPWG dosing guideline or drug-level clinical/variant annotations in PharmGKB for this molecule.

Molecules sharing ≥1 of this drug’s curated primary targets, merged from two biobtree sources and ranked by shared-target count, then clinical phase: ChEMBL clinical-stage candidates (development phase ≥2) and PubChem drug-class bioactivity (approved / known drugs acting on the target). Deduplicated by drug name; the drug’s own salt forms are excluded. Note: for a drug with few primary targets a shared-target match can reflect off-target / promiscuous binding rather than the same therapeutic mechanism — the phase ordering surfaces bona-fide therapeutics first.

278 molecules share ≥1 primary target. Top 60 by shared-target count:

MoleculeSourceStatusShared targets
AfatinibChEMBL + PubChemPhase 4 (approved)CDK19, CSF1R, FLT1, FLT3, KDR, KIT, LCK, NTRK3
CRIZOTINIBChEMBL + PubChemPhase 4 (approved)CDK19, CSF1R, FLT1, FLT3, KDR, KIT, LCK, NTRK3
FEDRATINIBChEMBL + PubChemPhase 4 (approved)CDK19, CSF1R, FLT1, FLT3, KDR, KIT, LCK, NTRK3
GEFITINIBChEMBL + PubChemPhase 4 (approved)CDK19, CSF1R, FLT1, FLT3, KDR, KIT, LCK, NTRK3
MIDOSTAURINChEMBL + PubChemPhase 4 (approved)CDK19, CSF1R, FLT1, FLT3, KDR, KIT, LCK, NTRK3
PAZOPANIBChEMBL + PubChemPhase 4 (approved)CDK19, CSF1R, FLT1, FLT3, KDR, KIT, LCK, NTRK3
QUIZARTINIBChEMBL + PubChemPhase 4 (approved)CDK19, CSF1R, FLT1, FLT3, KDR, KIT, LCK, NTRK3
SORAFENIBChEMBL + PubChemPhase 4 (approved)CDK19, CSF1R, FLT1, FLT3, KDR, KIT, LCK, NTRK3
SUNITINIBChEMBL + PubChemPhase 4 (approved)CDK19, CSF1R, FLT1, FLT3, KDR, KIT, LCK, NTRK3
DORAMAPIMODChEMBLPhase 2CDK19, CSF1R, FLT1, FLT3, KDR, KIT, LCK, NTRK3
FORETINIBChEMBLPhase 2CDK19, CSF1R, FLT1, FLT3, KDR, KIT, LCK, NTRK3
TOZASERTIBChEMBLPhase 2CDK19, CSF1R, FLT1, FLT3, KDR, KIT, LCK, NTRK3
SelumetinibPubChemApprovedCDK19, CSF1R, FLT1, FLT3, KDR, KIT, LCK, NTRK3
AXITINIBChEMBL + PubChemPhase 4 (approved)CDK19, CSF1R, FLT1, FLT3, KDR, KIT, LCK
PONATINIBChEMBL + PubChemPhase 4 (approved)CDK19, CSF1R, FLT1, FLT3, KDR, KIT, LCK
REGORAFENIBChEMBL + PubChemPhase 4 (approved)CSF1R, FLT1, FLT3, KDR, KIT, LCK, NTRK3
VANDETANIBChEMBL + PubChemPhase 4 (approved)CDK19, CSF1R, FLT1, FLT3, KDR, KIT, LCK
ENTRECTINIBChEMBLPhase 4 (approved)CSF1R, FLT1, FLT3, KDR, KIT, LCK, NTRK3
NINTEDANIBChEMBLPhase 4 (approved)CSF1R, FLT1, FLT3, KDR, KIT, LCK, NTRK3
DOVITINIBChEMBLPhase 3CSF1R, FLT1, FLT3, KDR, KIT, LCK, NTRK3
LESTAURTINIBChEMBLPhase 3CSF1R, FLT1, FLT3, KDR, KIT, LCK, NTRK3
LINIFANIBChEMBLPhase 3CDK19, CSF1R, FLT1, FLT3, KDR, KIT, NTRK3
ILORASERTIBChEMBLPhase 2CSF1R, FLT1, FLT3, KDR, KIT, LCK, NTRK3
R-406ChEMBLPhase 2CSF1R, FLT1, FLT3, KDR, KIT, LCK, NTRK3
RAF-265ChEMBLPhase 2CDK19, CSF1R, FLT1, FLT3, KDR, KIT, LCK
REBASTINIBChEMBLPhase 2CSF1R, FLT1, FLT3, KDR, KIT, LCK, NTRK3
SU-014813ChEMBLPhase 2CSF1R, FLT1, FLT3, KDR, KIT, LCK, NTRK3
TANDUTINIBChEMBLPhase 2CSF1R, FLT1, FLT3, KDR, KIT, LCK, NTRK3
BOSUTINIBChEMBL + PubChemPhase 4 (approved)CDK19, CSF1R, FLT3, KIT, LCK, NTRK3
ERLOTINIBChEMBL + PubChemPhase 4 (approved)CDK19, FLT1, FLT3, KDR, KIT, LCK
IMATINIBChEMBL + PubChemPhase 4 (approved)CDK19, CSF1R, FLT3, KDR, KIT, LCK
NILOTINIBChEMBL + PubChemPhase 4 (approved)CDK19, CSF1R, FLT3, KIT, LCK, NTRK3
DASATINIBChEMBLPhase 4 (approved)CSF1R, FLT1, FLT3, KDR, KIT, LCK
CEDIRANIBChEMBLPhase 3CSF1R, FLT1, FLT3, KDR, KIT, LCK
MOTESANIBChEMBLPhase 3CSF1R, FLT1, FLT3, KDR, KIT, LCK
CENISERTIBChEMBLPhase 2CSF1R, FLT1, FLT3, KDR, KIT, LCK
CEP-32496ChEMBLPhase 2CSF1R, FLT1, FLT3, KDR, KIT, LCK
DEFOSBARASERTIBChEMBLPhase 2CSF1R, FLT1, FLT3, KDR, KIT, LCK
IdelalisibPubChemApprovedCSF1R, FLT1, FLT3, KIT, LCK, NTRK3
NERATINIBChEMBL + PubChemPhase 4 (approved)CDK19, CSF1R, FLT3, KDR, LCK
BRIGATINIBChEMBLPhase 4 (approved)CSF1R, FLT3, KDR, KIT, LCK
CABOZANTINIBChEMBLPhase 4 (approved)FLT1, FLT3, KDR, KIT, LCK
INFIGRATINIBChEMBLPhase 4 (approved)FLT1, FLT3, KDR, KIT, LCK
TIVOZANIBChEMBLPhase 4 (approved)FLT1, FLT3, KDR, KIT, LCK
ALVOCIDIBChEMBLPhase 3CDK19, CSF1R, FLT3, KIT, LCK
BRIVANIBChEMBLPhase 3CSF1R, FLT1, KDR, KIT, LCK
CANERTINIBChEMBLPhase 3FLT1, FLT3, KDR, KIT, LCK
SEMAXANIBChEMBLPhase 3CSF1R, FLT1, FLT3, KDR, KIT
VATALANIBChEMBLPhase 3CDK19, CSF1R, FLT1, KDR, KIT
ENMD-2076ChEMBLPhase 2CSF1R, FLT3, KDR, KIT, LCK
CERITINIBChEMBLPhase 4 (approved)FLT3, KDR, KIT, LCK
IBRUTINIBChEMBLPhase 4 (approved)CSF1R, FLT3, KDR, LCK
ALISERTIBChEMBLPhase 3FLT1, KDR, LCK, NTRK3
BARASERTIBChEMBLPhase 3FLT3, KDR, KIT, LCK
DEFACTINIBChEMBLPhase 3FLT1, FLT3, KDR, NTRK3
SARACATINIBChEMBLPhase 3FLT3, KDR, KIT, LCK
VIMSELTINIBChEMBLPhase 3CSF1R, FLT3, KIT, LCK
AT-9283ChEMBLPhase 2FLT1, FLT3, KDR, LCK
BMS-754807ChEMBLPhase 2CSF1R, FLT3, LCK, NTRK3
BMS-777607ChEMBLPhase 2FLT3, KDR, KIT, LCK