Crystal Structure of FLT3 with a small molecule inhibitor

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.224 

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Characterizing and Overriding the Structural Mechanism of the Quizartinib-Resistant FLT3 "Gatekeeper" F691L Mutation with PLX3397.

Smith, C.C.Zhang, C.Lin, K.C.Lasater, E.A.Zhang, Y.Massi, E.Damon, L.E.Pendleton, M.Bashir, A.Sebra, R.Perl, A.Kasarskis, A.Shellooe, R.Tsang, G.Carias, H.Powell, B.Burton, E.A.Matusow, B.Zhang, J.Spevak, W.Ibrahim, P.N.Le, M.H.Hsu, H.H.Habets, G.West, B.L.Bollag, G.Shah, N.P.

(2015) Cancer Discov 5: 668-679

  • DOI: https://doi.org/10.1158/2159-8290.CD-15-0060
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Tyrosine kinase domain mutations are a common cause of acquired clinical resistance to tyrosine kinase inhibitors (TKI) used to treat cancer, including the FLT3 inhibitor quizartinib. Mutation of kinase "gatekeeper" residues, which control access to an allosteric pocket adjacent to the ATP-binding site, has been frequently implicated in TKI resistance. The molecular underpinnings of gatekeeper mutation-mediated resistance are incompletely understood. We report the first cocrystal structure of FLT3 with the TKI quizartinib, which demonstrates that quizartinib binding relies on essential edge-to-face aromatic interactions with the gatekeeper F691 residue, and F830 within the highly conserved Asp-Phe-Gly motif in the activation loop. This reliance makes quizartinib critically vulnerable to gatekeeper and activation loop substitutions while minimizing the impact of mutations elsewhere. Moreover, we identify PLX3397, a novel FLT3 inhibitor that retains activity against the F691L mutant due to a binding mode that depends less vitally on specific interactions with the gatekeeper position. We report the first cocrystal structure of FLT3 with a kinase inhibitor, elucidating the structural mechanism of resistance due to the gatekeeper F691L mutation. PLX3397 is a novel FLT3 inhibitor with in vitro activity against this mutation but is vulnerable to kinase domain mutations in the FLT3 activation loop.

  • Organizational Affiliation

    Division of Hematology/Oncology, University of California, San Francisco, California. Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor-type tyrosine-protein kinase FLT3415Homo sapiensMutation(s): 0 
Gene Names: FLT3CD135FLK2STK1
UniProt & NIH Common Fund Data Resources
Find proteins for P36888 (Homo sapiens)
Explore P36888 
Go to UniProtKB:  P36888
GTEx:  ENSG00000122025 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36888
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on P30

Download Ideal Coordinates CCD File 
B [auth A]1-(5-tert-butyl-1,2-oxazol-3-yl)-3-(4-{7-[2-(morpholin-4-yl)ethoxy]imidazo[2,1-b][1,3]benzothiazol-2-yl}phenyl)urea
C29 H32 N6 O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
P30 BindingDB:  4RT7 Kd: min: 1.3, max: 420 (nM) from 12 assay(s)
IC50: min: 0.51, max: 1330 (nM) from 24 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.224 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.88α = 90
b = 78.88β = 90
c = 138.36γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-22
    Type: Initial release
  • Version 1.1: 2015-06-17
    Changes: Database references