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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 75.34 kDa 
• Atom Count: 4992 
• Modelled Residue Count: 590 
• Deposited Residue Count: 654 
• Unique protein chains: 1

6GQJ

Crystal structure of human c-KIT kinase domain in complex with AZD3229-analogue (compound 18)

• DOI: 10.2210/pdb6GQJ/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-06-07 Released: 2018-09-19 
• Deposition Author(s): Schimpl, M., Hardy, C.J., Ogg, D.J., Overman, R.C., Packer, M.J., Kettle, J.G., Anjum, R., Barry, E., Bhavsar, D., Brown, C., Campbell, A., Goldberg, K., Grondine, M., Guichard, S., Hunt, T., Jones, O., Li, X., Moleva, O., Pearson, S., Shao, W., Smith, A., Smith, J., Stead, D., Stokes, S., Tucker, M., Ye, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 0.217 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

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

• PubMed: 30204441 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mast/stem cell growth factor receptor Kit	A, B	327	Homo sapiens	Mutation(s): 14  Gene Names: KIT, SCFR 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
F82	A, B	2-[4-(6,7-dimethoxyquinazolin-4-yl)oxy-2-methoxy-phenyl]-~{N}-(1-propan-2-ylpyrazol-4-yl)ethanamide C25 H27 N5 O5 INYIBEJMXPAZLV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 0.217 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.773	α = 90
b = 89.436	β = 90
c = 90.343	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-06-07 
• Released Date: 2018-09-19 
Deposition Author(s): Schimpl, M., Hardy, C.J., Ogg, D.J., Overman, R.C., Packer, M.J., Kettle, J.G., Anjum, R., Barry, E., Bhavsar, D., Brown, C., Campbell, A., Goldberg, K., Grondine, M., Guichard, S., Hunt, T., Jones, O., Li, X., Moleva, O., Pearson, S., Shao, W., Smith, A., Smith, J., Stead, D., Stokes, S., Tucker, M., Ye, Y.

Revision History  

• 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