Crystal structure of KIT kinase domain with a small molecule inhibitor, PLX3397

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Association of Combination of Conformation-Specific KIT Inhibitors With Clinical Benefit in Patients With Refractory Gastrointestinal Stromal Tumors: A Phase 1b/2a Nonrandomized Clinical Trial.

Wagner, A.J.Severson, P.L.Shields, A.F.Patnaik, A.Chugh, R.Tinoco, G.Wu, G.Nespi, M.Lin, J.Zhang, Y.Ewing, T.Habets, G.Burton, E.A.Matusow, B.Tsai, J.Tsang, G.Shellooe, R.Carias, H.Chan, K.Rezaei, H.Sanftner, L.Marimuthu, A.Spevak, W.Ibrahim, P.N.Inokuchi, K.Alcantar, O.Michelson, G.Tsiatis, A.C.Zhang, C.Bollag, G.Trent, J.C.Tap, W.D.

(2021) JAMA Oncol 7: 1343-1350

  • DOI: https://doi.org/10.1001/jamaoncol.2021.2086
  • Primary Citation of Related Structures:  
    7KHG, 7KHJ, 7KHK

  • PubMed Abstract: 

    Many cancer subtypes, including KIT-mutant gastrointestinal stromal tumors (GISTs), are driven by activating mutations in tyrosine kinases and may initially respond to kinase inhibitors but frequently relapse owing to outgrowth of heterogeneous subclones with resistance mutations. KIT inhibitors commonly used to treat GIST (eg, imatinib and sunitinib) are inactive-state (type II) inhibitors.

  • Organizational Affiliation

    Plexxikon Inc, Berkeley, California.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mast/stem cell growth factor receptor Kit335Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P10721 (Homo sapiens)
Explore P10721 
Go to UniProtKB:  P10721
PHAROS:  P10721
GTEx:  ENSG00000157404 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10721
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P31 (Subject of Investigation/LOI)
Query on P31

Download Ideal Coordinates CCD File 
B [auth A]5-[(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)methyl]-N-{[6-(trifluoromethyl)pyridin-3-yl]methyl}pyridin-2-amine
C20 H15 Cl F3 N5
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.133α = 90
b = 81.961β = 107.6
c = 50.061γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2021-07-07 
  • Deposition Author(s): Zhang, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2021-08-04
    Changes: Database references
  • Version 1.2: 2021-08-11
    Changes: Database references
  • Version 1.3: 2021-09-29
    Changes: Database references
  • Version 1.4: 2023-10-18
    Changes: Data collection, Refinement description