9N6G | pdb_00009n6g

EGFR(T790M/V948R) in complex with LN2827

• PDB DOI: https://doi.org/10.2210/pdb9N6G/pdb

• Classification: TRANSFERASE
• Organism(s): Spodoptera frugiperda
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2025-02-05 Released: 2025-08-13 
• Deposition Author(s): Chitnis, S.P., Hartman, T.J., Heppner, D.E.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)

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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

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

• PubMed: 40665765 
• DOI: https://doi.org/10.1002/ardp.70027
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York, USA.
Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany.
Department of Medicinal Chemistry, Faculty of Medicine, Institute for Biomedical Engineering, Eberhard Karls Universität Tübingen, Tübingen, Germany.
Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.
Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls Universität Tübingen, Tübingen, Germany.
Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Tübingen, Germany.
Department of Structural Biology, University at Buffalo, The State University of New York, Buffalo, New York, USA.
Department of Pharmaceutical Sciences, University at Buffalo, The State University of New York, Buffalo, New York, USA.
Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 150.21 kDa 
• Atom Count: 8,948 
• Modeled Residue Count: 1,124 
• Deposited Residue Count: 1,308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A [auth D], B [auth A], C [auth B], D [auth C]	327	Spodoptera frugiperda	Mutation(s): 0  EC: 2.7.10.1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BWA	E [auth D], F [auth A], G [auth B], H [auth C]	N-{(3P)-3-[(4P)-5-(2-acetamidopyridin-4-yl)-2-(methylsulfanyl)-1H-imidazol-4-yl]phenyl}-2,6-difluorobenzamide C24 H19 F2 N5 O2 S XSGKACFQFCCIJV-UHFFFAOYSA-N

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 = 71.468	α = 90
b = 101.884	β = 102.549
c = 87.726	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
DIALS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Chitnis, S.P., Hartman, T.J., Heppner, D.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM155353
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)	United States	UL1TR001412-08

Revision History  

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