4RT7

Crystal Structure of FLT3 with a small molecule inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.224 

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
  • Primary Citation of Related Structures:  
    4RT7

  • 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. Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California. nshah@medicine.ucsf.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor-type tyrosine-protein kinase FLT3A415Homo sapiensMutation(s): 0 
Gene Names: FLT3CD135FLK2STK1
EC: 2.7.10.1
Find proteins for P36888 (Homo sapiens)
Explore P36888 
Go to UniProtKB:  P36888
NIH Common Fund Data Resources
PHAROS  P36888
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P30
Query on P30

Download Ideal Coordinates 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
C29 H32 N6 O4 S
CVWXJKQAOSCOAB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
P30IC50:  30   nM  BindingDB
P30IC50:  120   nM  BindingDB
P30Kd:  2.200000047683716   nM  BindingDB
P30Kd:  8.800000190734863   nM  BindingDB
P30IC50:  93   nM  BindingDB
P30IC50:  26   nM  BindingDB
P30IC50:  10   nM  BindingDB
P30IC50:  15.899999618530273   nM  BindingDB
P30IC50:  39   nM  BindingDB
P30IC50:  4.199999809265137   nM  BindingDB
P30Kd:  1.2999999523162842   nM  BindingDB
P30IC50:  2   nM  BindingDB
P30IC50:  136   nM  BindingDB
P30IC50:  36   nM  BindingDB
P30IC50:  137   nM  BindingDB
P30Kd:  3.700000047683716   nM  BindingDB
P30Kd:  7.099999904632568   nM  BindingDB
P30Kd:  5.099999904632568   nM  BindingDB
P30Kd:  1.600000023841858   nM  BindingDB
P30Kd:  4.099999904632568   nM  BindingDB
P30IC50:  69   nM  BindingDB
P30IC50:  72   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
MOLREPphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



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
    Changes: Database references