9EWT | pdb_00009ewt

Optimisation of Potent, Efficacious, Selective and Blood-Brain Barrier Penetrating Inhibitors Targeting EGFR Exon20 Insertion Mutations


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 
    0.342 (Depositor), 0.316 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.238 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9EWT

Ligand Structure Quality Assessment 


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Literature

Optimization of Potent, Efficacious, Selective and Blood-Brain Barrier Penetrating Inhibitors Targeting EGFR Exon20 Insertion Mutations.

Thomson, C.Braybrooke, E.Colclough, N.Davies, N.L.Floc'h, N.Greenwood, R.Guerot, C.Hargreaves, D.Johnstrom, P.Khurana, P.Kostomiris, D.H.Li, S.Lister, A.Lorthioir, O.Martin, S.McCoull, W.McLean, N.J.McWilliams, L.Orme, J.P.Packer, M.J.Pearson, S.Swaih, A.M.Tentarelli, S.Tucker, M.J.Ward, R.A.Wilkinson, S.Winlow, P.Wood, I.L.

(2024) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01792
  • Primary Citation Related Structures: 
    9EWS, 9EWT

  • PubMed Abstract: 

    Herein, we report the optimization of a series of epidermal growth factor receptor (EGFR) Exon20 insertion (Ex20Ins) inhibitors using structure-based drug design (SBDD), leading to the discovery of compound 28 , a potent and wild type selective molecule, which demonstrates efficacy in multiple EGFR Ex20Ins xenograft models and blood-brain barrier penetration in preclinical species. Building on our earlier discovery of an in vivo probe, SBDD was used to design a novel bicyclic core with a lower molecular weight to facilitate blood-brain barrier penetration. Further optimization including strategic linker replacement and diversification of the ring system interacting with the c-helix enabled photolytic and metabolic stability improvements. Together with refinement of molecular properties important for achieving high brain exposure, including molecular weight, H-bonding, and polarity, 28 was identified.


  • Organizational Affiliation
    • Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0AA, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 76.45 kDa 
  • Atom Count: 4,463 
  • Modeled Residue Count: 546 
  • Deposited Residue Count: 664 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor
A, B
332Homo 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

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H7O
(Subject of Investigation/LOI)

Query on A1H7O



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
1-[2-[3-[(E)-2-(5-cyclopropyl-1,3-oxazol-2-yl)ethenyl]phenyl]-3-pyridin-4-yl-4,6-dihydropyrrolo[3,4-d]imidazol-5-yl]propan-1-one
C27 H25 N5 O2
DWPDTMOTWBPAEZ-RMKNXTFCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free:  0.342 (Depositor), 0.316 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.238 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.421α = 90
b = 99.845β = 114.08
c = 85.196γ = 90
Software Package:
Software NamePurpose
autoPROCdata reduction
STARANISOdata scaling
BUSTERrefinement
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release