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 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: 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
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