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 9PWI | pdb_00009pwi

EGFR kinase bound to ZNL-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.254 (Depositor), 0.265 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9PWI

This is version 1.0 of the entry. See complete history. 

Literature

Overcoming EGFR resistance by monovalent and bident inhibitors targeting Cys775.

Li, Z., Jiang, J., Wang, Y., Ficarro, S.B., Collins, S.J., Beyett, T.S., Schaeffner, I.K., Tavares, I., Gottlieb, F.H., Suda, D., Gokhale, P.C., Black-Holmes, L.M., Gazgalis, D., Eck, M.J., Janne, P.A., Marto, J.A., Che, J., Gray, N.S., Zhang, T.

(2025) bioRxiv 

  • DOI: https://doi.org/10.64898/2025.11.28.691243
  • Primary Citation Related Structures: 
    9PWI

  • PubMed Abstract: 

    Covalent targeting of EGFR cysteine 797 by osimertinib is one of the most successful breakthroughs in targeted therapy, fundamentally transforming the treatment landscape for non-small cell lung cancer (NSCLC) patients. However, resistance driven by mutation of C797 remains a major clinical challenge. Developing novel covalent strategies beyond C797 targeting presents a compelling opportunity for next-generation EGFR inhibitors. We first demonstrated that cysteine 775, located deep within the ATP-binding pocket, is accessible by a rationally designed covalent molecule ZNL-3, which as the first-in-class covalent cysteine 775 inhibitor exhibited strong efficacy in osimertinib-resistant mouse models. To further enhance resilience to resistance-causing mutations, we developed a dual-warhead, bident compound-YNW-1-which covalently targets both cysteine 775 and 797 simultaneously. YNW-1 is the first intramolecular lock to exhibit balanced reactive efficiency on both cysteines, rendering single-site mutations ineffective to confer resistance. The discovery of ZNL-3 and YNW-1 represents significant advancements in EGFR-targeted drug development, and further optimization toward clinical translation is a worthwhile strategy. SIGNIFICANCE: This study establishes the therapeutic potential of an EGFR covalent inhibitor through unprecedented targeting of cysteine 775 and provides the first demonstration that dual cysteine engagement offers superior efficacy over conventional covalent inhibitors by delaying resistance.

Macromolecule Content 

  • Total Structure Weight: 38.15 kDa 
  • Atom Count: 2,243 
  • Modeled Residue Count: 274 
  • Deposited Residue Count: 331 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor331Homo sapiensMutation(s): 0 
Gene Names: EGFR, ERBB, ERBB1, HER1
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
A1CMF(
Subject of Investigation/LOI)

Query on A1CMF



Download:Ideal Coordinates CCD File
B [auth A]N-[2-({1-methyl-7-[4-(4-methylpiperazin-1-yl)anilino]-2-oxo-1,4-dihydropyrimido[4,5-d]pyrimidin-3(2H)-yl}methyl)phenyl]prop-2-enamide
C28 H32 N8 O2
NGHZZCITSZEFOQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.254 (Depositor), 0.265 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.391α = 90
b = 70.391β = 90
c = 161.719γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States5R01CA116020-16

Revision History  (Full details and data files)

  • Version 1.0: 2026-10-28
    Type: Initial release