8HV7

Crystal structure of EGFR_TMX in complex with covalently bound fragment 9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.222 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A covalent fragment-based strategy targeting a novel cysteine to inhibit activity of mutant EGFR kinase.

Kuki, N.Walmsley, D.L.Kanai, K.Takechi, S.Yoshida, M.Murakami, R.Takano, K.Tominaga, Y.Takahashi, M.Ito, S.Nakao, N.Angove, H.Baker, L.M.Carter, E.Dokurno, P.Le Strat, L.Macias, A.T.Molyneaux, C.A.Murray, J.B.Surgenor, A.E.Hamada, T.Hubbard, R.E.

(2023) RSC Med Chem 14: 2731-2737

  • DOI: https://doi.org/10.1039/d3md00439b
  • Primary Citation of Related Structures:  
    8HV1, 8HV2, 8HV3, 8HV4, 8HV5, 8HV6, 8HV7, 8HV8, 8HV9, 8HVA

  • PubMed Abstract: 

    Several generations of ATP-competitive anti-cancer drugs that inhibit the activity of the intracellular kinase domain of the epidermal growth factor receptor (EGFR) have been developed over the past twenty years. The first-generation of drugs such as gefitinib bind reversibly and were followed by a second-generation such as dacomitinib that harbor an acrylamide moiety that forms a covalent bond with C797 in the ATP binding pocket. Resistance emerges through mutation of the T790 gatekeeper residue to methionine, which introduces steric hindrance to drug binding and increases the K m for ATP. A third generation of drugs, such as osimertinib were developed which were effective against T790M EGFR in which an acrylamide moiety forms a covalent bond with C797, although resistance has emerged by mutation to S797. A fragment-based screen to identify new starting points for an EGFR inhibitor serendipitously identified a fragment that reacted with C775, a previously unexploited residue in the ATP binding pocket for a covalent inhibitor to target. A number of acrylamide containing fragments were identified that selectively reacted with C775. One of these acrylamides was optimized to a highly selective inhibitor with sub-1 μM activity, that is active against T790M, C797S mutant EGFR independent of ATP concentration, providing a potential new strategy for pan-EGFR mutant inhibition.


  • Organizational Affiliation

    R&D Division Daiichi Sankyo Co., Ltd. Shinagawa-ku Tokyo 140-8710 Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor331Homo sapiensMutation(s): 6 
Gene Names: EGFRERBBERBB1HER1
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00533 (Homo sapiens)
Explore P00533 
Go to UniProtKB:  P00533
PHAROS:  P00533
GTEx:  ENSG00000146648 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00533
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.222 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.874α = 90
b = 144.874β = 90
c = 144.874γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2023-12-13 
  • Deposition Author(s): Dokurno, P.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-13
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Structure summary