Crystal structure of the kinase domain of human c-KIT with a cyclic imidate inhibitor covalently bound to Cys788

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

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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

  • DOI: https://doi.org/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, Waltham, Massachusetts 02451, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mast/stem cell growth factor receptor Kit,Mast/stem cell growth factor receptor Kit
A, B
328Homo sapiensMutation(s): 14 
Gene Names: KITSCFR
UniProt & NIH Common Fund Data Resources
Find proteins for P10721 (Homo sapiens)
Explore P10721 
Go to UniProtKB:  P10721
GTEx:  ENSG00000157404 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10721
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
O2H (Subject of Investigation/LOI)
Query on O2H

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C31 H32 N4 O5
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.71α = 90
b = 90.272β = 90
c = 91.178γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

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