Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 75.64 kDa 
• Atom Count: 4843 
• Modelled Residue Count: 598 
• Deposited Residue Count: 656 
• Unique protein chains: 1

6XV9

Crystal structure of the kinase domain of human c-KIT in complex with a type-II inhibitor

• PDB DOI: 10.2210/pdb6XV9/pdb

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


• Deposited: 2020-01-21 Released: 2020-05-27 
• Deposition Author(s): Ogg, D.J., Howard, T., McAuley, K., Hoyt, E.A., Thomas, M., Bodnarchuk, M.S., Lewis, H.J., Barratt, D., Deery, M.J., Bernardes, G.J.L., Ward, R.A., Kettle, J.G., Waring, M.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.38 Å
• R-Value Free: 0.247 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Literature

Alkynyl Benzoxazines and Dihydroquinazolines as Cysteine Targeting Covalent Warheads and Their Application in Identification of Selective Irreversible Kinase Inhibitors.

McAulay, K., Hoyt, E.A., Thomas, M., Schimpl, M., Bodnarchuk, M.S., Lewis, H.J., Barratt, D., Bhavsar, D., Robinson, D.M., Deery, M.J., Ogg, D.J., Bernardes, G.J.L., Ward, R.A., Waring, M.J., Kettle, J.G.

(2020) J Am Chem Soc 142: 10358-10372

• PubMed: 32412754 
• DOI: 10.1021/jacs.9b13391
• Primary Citation of Related Structures:  
  6XV9, 6XVA, 6XVB, 6XVJ, 6XVK


• PubMed Abstract: 
  

With a resurgence in interest in covalent drugs, there is a need to identify new moieties capable of cysteine bond formation that are differentiated from commonly employed systems such as acrylamide. Herein, we report on the discovery of new alkynyl benzoxazine and dihydroquinazoline moieties capable of covalent reaction with cysteine. Their utility as alternative electrophilic warheads for chemical biological probes and drug molecules is demonstrated through site-selective protein modification and incorporation into kinase drug scaffolds. A potent covalent inhibitor of JAK3 kinase was identified with superior selectivity across the kinome and improvements in in vitro pharmacokinetic profile relative to the related acrylamide-based inhibitor. In addition, the use of a novel heterocycle as a cysteine reactive warhead is employed to target Cys788 in c-KIT, where acrylamide has previously failed to form covalent interactions. These new reactive and selective heterocyclic warheads supplement the current repertoire for cysteine covalent modification while avoiding some of the limitations generally associated with established moieties.

---

Organizational Affiliation: 

Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mast/stem cell growth factor receptor Kit,Mast/stem cell growth factor receptor Kit	A, B	328	Homo sapiens	Mutation(s): 14  Gene Names: KIT, SCFR EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P10721 (Homo sapiens) Explore P10721  Go to UniProtKB:  P10721
PHAROS:  P10721

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O35 (Subject of Investigation/LOI)	C [auth A], D [auth B]	~{N}-[3-[(dimethylamino)methyl]-5-methyl-phenyl]-2-[3-methoxy-5-(7-methoxyquinolin-4-yl)oxy-pyridin-2-yl]ethanamide C28 H30 N4 O4 MALCRTBNJLPDJJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.38 Å
• R-Value Free: 0.247 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.632	α = 90
b = 90.614	β = 90
c = 87.042	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2020-01-21 
• Released Date: 2020-05-27 
Deposition Author(s): Ogg, D.J., Howard, T., McAuley, K., Hoyt, E.A., Thomas, M., Bodnarchuk, M.S., Lewis, H.J., Barratt, D., Deery, M.J., Bernardes, G.J.L., Ward, R.A., Kettle, J.G., Waring, M.J.

Revision History  

• Version 1.0: 2020-05-27
  Type: Initial release
  
• Version 1.1: 2020-06-17
  Changes: Database references