9GDV | pdb_00009gdv

Highly optimized CNS penetrant inhibitors of EGFR Exon20 Insertion Mutations


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 
    0.293 (Depositor), 0.286 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted Q6KClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Highly Optimized CNS Penetrant Inhibitors of EGFR Exon20 Insertion Mutations.

McCoull, W.Thomson, C.Braybrooke, E.Chan, C.Colclough, N.Cortes Gonzalez, M.A.Cosulich, S.Davies, N.L.Floc'h, N.Greenwood, R.Hargreaves, D.Huang, P.Hunt, T.A.Johnson, T.Johnstrom, P.Kettle, J.G.Kondrashov, M.Kostomiris, D.H.Li, S.Lister, A.Martin, S.McKerrecher, D.McLean, N.Nissink, J.W.M.Orme, J.P.Orwig, P.Packer, M.J.Pearson, S.Qin, L.Felisberto-Rodrigues, C.Savoca, A.Schou, M.Stokes, S.Swaih, A.M.Talbot, S.Tucker, M.J.Ward, R.A.Wadforth, E.Wang, C.Wilson, J.Yang, Y.

(2025) J Med Chem 68: 3700-3748

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02811
  • Primary Citation of Related Structures:  
    9GC4, 9GC5, 9GC6, 9GDV, 9HBO

  • PubMed Abstract: 

    Despite recent advances in the inhibition of EGFR (epidermal growth factor receptor), there remains a clinical need for new EGFR Exon20 insertion (Ex20Ins) inhibitors that spare EGFR WT. Herein, we report the discovery and optimization of two chemical series leading to ether 23 and biaryl 36 as potent, selective, and brain-penetrant inhibitors of Ex20Ins mutants. Building on our earlier discovery of alkyne 5 which allowed access to CNS property space for an Ex20Ins inhibitor, we utilized structure-based design to move to lower lipophilicity and lower CL int compounds while maintaining a WT selectivity margin. During optimization, aldehyde oxidase (AO) metabolism was identified as a human clearance risk, and through SAR exploration, lower AO metabolism was achieved. Potency and WT margin were optimized across a range of Ex20Ins mutants including the potential acquired resistance T790M mutant and efficacy demonstrated in an LXF2478 Ex20Ins ASV model with margin to EGFR WT in vivo.


  • Organizational Affiliation

    AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0AA, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor
A, B
330Homo sapiensMutation(s): 1 
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: 2.22 Å
  • R-Value Free:  0.293 (Depositor), 0.286 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.025α = 90
b = 82.31β = 90
c = 89.297γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
BUSTERrefinement
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted Q6KClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release
  • Version 1.1: 2025-02-26
    Changes: Database references