9JQ1 | pdb_00009jq1

Crystal structure of EGFR T790M/C797S/L858R mutant in complex with 2,2-dichloro-N-(5-((5-chloro-4-((2-(dimethylphosphoryl)phenyl)amino)pyrimidin-2-yl)amino)-4-methoxy-2-(4-(4-methylpiperazin-1-yl)piperidin-1-yl)phenyl)acetamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 
    0.274 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9JQ1

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

A Dichloropropionamide-Substituted Diaminopyrimidine EGFR-TKI Overcomes Osimertinib Resistance in NSCLC via Dual Anchoring at Ser797 and Met793.

Wang, Y.Yu, Q.Yang, X.Ma, L.Huang, R.Chen, H.Jiang, Z.Wu, Z.Wu, C.Deng, X.Wang, J.Li, W.He, Y.

(2026) J Med Chem 69: 625-659

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c02807
  • Primary Citation Related Structures: 
    9JQ1

  • PubMed Abstract: 

    The tertiary C797S mutation in the EGFR tyrosine kinase domain disrupts osimertinib binding, driving resistance in NSCLC. We designed a series of novel diaminopyrimidine derivatives to establish the interaction with Ser797. H8b potently inhibited EGFR L858R/T790M/C797S kinase with an IC 50 of 3.86 nM (30-fold lower than osimertinib) and suppressed both double mutant NCI-H1975 and triple mutant H1975-M3 cells with IC 50 s of 0.03 μM and 0.57 μM (14- and 11-fold reductions over osimertinib, respectively). Cocrystal X-ray analysis revealed that H8b forms a "two-point tethering" in the ATP pocket with a hydrogen bond between its dichloropropionamide oxygen and Ser797, complemented by a hydrogen bond between terminal N of the piperazine ring and Phe795. Mechanistically, H8b suppressed EGFR phosphorylation and downstream AKT, STAT3, and MAPK signaling, inhibiting proliferation, invasion, and migration. In vivo , H8b achieved 71.15% tumor inhibition in H1975-M3 xenografts. This study identifies H8b as a promising EGFR-TKI overcoming C797S-mediated resistance.


  • Organizational Affiliation
    • Department of Pulmonary and Critical Care Medicine, West China Hospital, State Key Laboratory of Respiratory Health and Multimorbidity, Sichuan University, Chengdu, Sichuan 610041, China.

Macromolecule Content 

  • Total Structure Weight: 38.22 kDa 
  • Atom Count: 2,450 
  • Modeled Residue Count: 301 
  • Deposited Residue Count: 329 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor329Homo sapiensMutation(s): 3 
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
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
A1ECU
(Subject of Investigation/LOI)

Query on A1ECU



Download:Ideal Coordinates CCD File
B [auth A]2,2-bis(chloranyl)-~{N}-[5-[[5-chloranyl-4-[(2-dimethylphosphorylphenyl)amino]pyrimidin-2-yl]amino]-4-methoxy-2-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl]ethanamide
C31 H40 Cl3 N8 O3 P
WKUTZQYPDRJNAE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free:  0.274 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.01α = 90
b = 146.01β = 90
c = 146.01γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Cootmodel building
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82373721

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2026-07-15
    Changes: Database references