6GQM

Crystal structure of human c-KIT kinase domain in complex with a small molecule inhibitor, AZD3229


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery of N-(4-{[5-Fluoro-7-(2-methoxyethoxy)quinazolin-4-yl]amino}phenyl)-2-[4-(propan-2-yl)-1 H-1,2,3-triazol-1-yl]acetamide (AZD3229), a Potent Pan-KIT Mutant Inhibitor for the Treatment of Gastrointestinal Stromal Tumors.

Kettle, J.G.Anjum, R.Barry, E.Bhavsar, D.Brown, C.Boyd, S.Campbell, A.Goldberg, K.Grondine, M.Guichard, S.Hardy, C.J.Hunt, T.Jones, R.D.O.Li, X.Moleva, O.Ogg, D.Overman, R.C.Packer, M.J.Pearson, S.Schimpl, M.Shao, W.Smith, A.Smith, J.M.Stead, D.Stokes, S.Tucker, M.Ye, Y.

(2018) J Med Chem 61: 8797-8810

  • DOI: 10.1021/acs.jmedchem.8b00938
  • Primary Citation of Related Structures:  
    6GQQ, 6GQP, 6GQK, 6GQJ, 6GQM, 6GQL, 6GQO

  • PubMed Abstract: 
  • While the treatment of gastrointestinal stromal tumors (GISTs) has been revolutionized by the application of targeted tyrosine kinase inhibitors capable of inhibiting KIT-driven proliferation, diverse mutations to this kinase drive resistance to established therapies ...

    While the treatment of gastrointestinal stromal tumors (GISTs) has been revolutionized by the application of targeted tyrosine kinase inhibitors capable of inhibiting KIT-driven proliferation, diverse mutations to this kinase drive resistance to established therapies. Here we describe the identification of potent pan-KIT mutant kinase inhibitors that can be dosed without being limited by the tolerability issues seen with multitargeted agents. This effort focused on identification and optimization of an existing kinase scaffold through the use of structure-based design. Starting from a series of previously reported phenoxyquinazoline and quinoline based inhibitors of the tyrosine kinase PDGFRα, potency against a diverse panel of mutant KIT driven Ba/F3 cell lines was optimized, with a particular focus on reducing activity against a KDR driven cell model in order to limit the potential for hypertension commonly seen in second and third line GIST therapies. AZD3229 demonstrates potent single digit nM growth inhibition across a broad cell panel, with good margin to KDR-driven effects. Selectivity over KDR can be rationalized predominantly by the interaction of water molecules with the protein and ligand in the active site, and its kinome selectivity is similar to the best of the approved GIST agents. This compound demonstrates excellent cross-species pharmacokinetics, shows strong pharmacodynamic inhibition of target, and is active in several in vivo models of GIST.


    Organizational Affiliation

    Pharmaron Beijing Co., Ltd. , 6 Taihe Road BDA , Beijing 100176 , P. R. China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mast/stem cell growth factor receptor Kit AB328Homo sapiensMutation(s): 14 
Gene Names: KITSCFR
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F8H
Query on F8H

Download Ideal Coordinates CCD File 
A, B
~{N}-[4-[[5-fluoranyl-7-(2-methoxyethoxy)quinazolin-4-yl]amino]phenyl]-2-(4-propan-2-yl-1,2,3-triazol-1-yl)ethanamide
C24 H26 F N7 O3
FLJOFQUXYAWOPE-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.97α = 90
b = 90.18β = 90
c = 91.15γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-10-03
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-31
    Changes: Data collection, Database references