3G0F

KIT kinase domain mutant D816H in complex with sunitinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

KIT kinase mutants show unique mechanisms of drug resistance to imatinib and sunitinib in gastrointestinal stromal tumor patients.

Gajiwala, K.S.Wu, J.C.Christensen, J.Deshmukh, G.D.Diehl, W.DiNitto, J.P.English, J.M.Greig, M.J.He, Y.A.Jacques, S.L.Lunney, E.A.McTigue, M.Molina, D.Quenzer, T.Wells, P.A.Yu, X.Zhang, Y.Zou, A.Emmett, M.R.Marshall, A.G.Zhang, H.M.Demetri, G.D.

(2009) Proc.Natl.Acad.Sci.USA 106: 1542-1547

  • DOI: 10.1073/pnas.0812413106
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Most gastrointestinal stromal tumors (GISTs) exhibit aberrant activation of the receptor tyrosine kinase (RTK) KIT. The efficacy of the inhibitors imatinib mesylate and sunitinib malate in GIST patients has been linked to their inhibition of these mu ...

    Most gastrointestinal stromal tumors (GISTs) exhibit aberrant activation of the receptor tyrosine kinase (RTK) KIT. The efficacy of the inhibitors imatinib mesylate and sunitinib malate in GIST patients has been linked to their inhibition of these mutant KIT proteins. However, patients on imatinib can acquire secondary KIT mutations that render the protein insensitive to the inhibitor. Sunitinib has shown efficacy against certain imatinib-resistant mutants, although a subset that resides in the activation loop, including D816H/V, remains resistant. Biochemical and structural studies were undertaken to determine the molecular basis of sunitinib resistance. Our results show that sunitinib targets the autoinhibited conformation of WT KIT and that the D816H mutant undergoes a shift in conformational equilibrium toward the active state. These findings provide a structural and enzymologic explanation for the resistance profile observed with the KIT inhibitors. Prospectively, they have implications for understanding oncogenic kinase mutants and for circumventing drug resistance.


    Organizational Affiliation

    Departments of Structural and Computational Biology, Cancer Biology, and Biochemical Pharmacology, Pfizer Global Research and Development, 10777 Science Center Drive, La Jolla, CA 92121, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mast/stem cell growth factor receptor
A, B
336Homo sapiensMutation(s): 1 
Gene Names: KIT (SCFR)
EC: 2.7.10.1
Find proteins for P10721 (Homo sapiens)
Go to Gene View: KIT
Go to UniProtKB:  P10721
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
B49
Query on B49

Download SDF File 
Download CCD File 
A, B
N-[2-(diethylamino)ethyl]-5-[(Z)-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-3-carboxamide
SUNITINIB
C22 H27 F N4 O2
WINHZLLDWRZWRT-ATVHPVEESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B49Kd: 22 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.462α = 90.00
b = 101.783β = 90.00
c = 105.505γ = 90.00
Software Package:
Software NamePurpose
CNXphasing
CNXrefinement
SCALEPACKdata scaling
HKL-2000data reduction
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-08-16
    Type: Refinement description, Source and taxonomy