4RT7

Crystal Structure of FLT3 with a small molecule inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1158/2159-8290.CD-15-0060

  • 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 ...

    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.


    Organizational Affiliation

    Division of Hematology/Oncology, University of California, San Francisco, California.,Plexxikon Inc., Berkeley, California.,Division of Hematology/Oncology, University of California, San Francisco, California. Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.,Division of Hematology/Oncology, University of California, San Francisco, California. Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California. nshah@medicine.ucsf.edu.,Icahn Institute for Genomics and Multiscale Biology, Mount Sinai School of Medicine, New York, New York.,Abramson Cancer Center of the University of Pennsylvania, Philadelphia, Pennsylvania.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Receptor-type tyrosine-protein kinase FLT3
A
415Homo sapiensMutation(s): 0 
Gene Names: FLT3 (CD135, FLK2, STK1)
EC: 2.7.10.1
Find proteins for P36888 (Homo sapiens)
Go to Gene View: FLT3
Go to UniProtKB:  P36888
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P30
Query on P30

Download SDF File 
Download CCD File 
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
Quizartinib, PLX3397
C29 H32 N6 O4 S
CVWXJKQAOSCOAB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
P30IC50: 2 - 137 nM (100) BINDINGDB
P30Kd: 1.3 - 8.8 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.218 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 78.880α = 90.00
b = 78.880β = 90.00
c = 138.360γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
MOSFLMdata reduction
Blu-Icedata collection
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-11-13 
  • Released Date: 2015-04-22 
  • Deposition Author(s): Zhang, Y., Zhang, C.

Revision History 

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