Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.62 kDa 
• Atom Count: 3022 
• Modelled Residue Count: 332 
• Deposited Residue Count: 336 
• Unique protein chains: 1

3G0E

KIT kinase domain in complex with sunitinib

• DOI: 10.2210/pdb3G0E/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2009-01-27 Released: 2009-02-24 
• Deposition Author(s): Gajiwala, K.S., Wu, J.C., Lunney, E.A., Gemetri, G.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.212 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 

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

• PubMed: 19164557 
• DOI: 10.1073/pnas.0812413106
• Primary Citation of Related Structures:  
  3G0E, 3G0F


• 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 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mast/stem cell growth factor receptor	A	336	Homo sapiens	Mutation(s): 0  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 GTEx:  ENSG00000157404

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B49	A	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
B49	Kd:  20   nM  Binding MOAD
B49	Kd :  20   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.212 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.033	α = 90
b = 80.973	β = 90
c = 93.32	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
CNX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-01-27 
• Released Date: 2009-02-24 
Deposition Author(s): Gajiwala, K.S., Wu, J.C., Lunney, E.A., Gemetri, G.D.

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: Data collection, Refinement description, Source and taxonomy