3G0F

KIT kinase domain mutant D816H in complex with sunitinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

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 U S A 106: 1542-1547

  • DOI: 10.1073/pnas.0812413106
  • Structures With Same Primary Citation

  • 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 receptorA, B336Homo sapiensMutation(s): 1 
Gene Names: KIT
EC: 2.7.10.1
Find proteins for P10721 (Homo sapiens)
Explore P10721 
Go to UniProtKB:  P10721
NIH Common Fund Data Resources
PHAROS  P10721
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B49
Query on B49

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-carbo xamide
C22 H27 F N4 O2
WINHZLLDWRZWRT-ATVHPVEESA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B49Kd :  22   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.462α = 90
b = 101.783β = 90
c = 105.505γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
CNXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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