9N6G | pdb_00009n6g

EGFR(T790M/V948R) in complex with LN2827


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 
    0.253 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.210 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structure-Activity Relationships of Inactive-Conformation Binding EGFR Inhibitors: Linking the ATP and Allosteric Pockets.

Chitnis, S.P.Wittlinger, F.Mollers, M.Hartman, T.J.Gunther, M.Eck, M.J.Laufer, S.A.Heppner, D.E.

(2025) Arch Pharm (Weinheim) 358: e70027-e70027

  • DOI: https://doi.org/10.1002/ardp.70027
  • Primary Citation of Related Structures:  
    9N6G

  • PubMed Abstract: 

    The epidermal growth factor receptor (EGFR) tyrosine kinase is an important therapeutic target in non-small cell lung cancer (NSCLC). However, the continual emergence of resistance mutations in the treatment of EGFR mutation-positive NSCLC with currently approved tyrosine kinase inhibitors warrants the development of next-generation inhibitors. Since research for ATP-competitive EGFR tyrosine kinase inhibitors (TKIs) that extend into the back pocket has been neglected in the recent past, we survey the extent to which such binding functional groups can be incorporated into an ATP-site imidazole scaffold. We find that meta-substituted amide linkers derivatized with fluorine in 2,6-positions and/or a hydroxy group in 3-position of the back pocket phenyl exhibit the highest potency. Structural insights into how the back pocket groups are bound through points of connection provide new directions for the discovery and optimization of inactive conformation targeting agents in EGFR and other kinases.


  • Organizational Affiliation
    • Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptorA [auth D],
B [auth A],
C [auth B],
D [auth C]
327Spodoptera frugiperdaMutation(s): 0 
EC: 2.7.10.1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free:  0.253 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.210 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.468α = 90
b = 101.884β = 102.549
c = 87.726γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM155353
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)United StatesUL1TR001412-08

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-13
    Type: Initial release