Crystal structure of EGFR 696-1022 L858R in complex with CO-1686

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

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Structural basis of mutant-selectivity and drug-resistance related to CO-1686.

Yan, X.E.Zhu, S.J.Liang, L.Zhao, P.Choi, H.G.Yun, C.H.

(2017) Oncotarget 8: 53508-53517

  • DOI: https://doi.org/10.18632/oncotarget.18588
  • Primary Citation of Related Structures:  
    5XDK, 5XDL

  • PubMed Abstract: 

    Non-small-cell lung cancers (NSCLCs) caused by activating mutations in the kinase domain of epidermal growth factor receptor (EGFR) initially respond to first-generation reversible drugs gefitinib and erlotinib. However, clinical efficacy is limited due to the development of drug-resistance that in more than half of the cases are driven by the secondary T790M mutation. CO-1686 is one of the third generation irreversible inhibitors that inhibits EGFR activating mutants, including those with concurrent T790M, while avoiding the off-target toxicity owing to inhibition of wild-type EGFR in treating EGFR mutation-positive NSCLCs. Despite the remarkable success, the experimentally determined structure of this agent in complex with EGFR T790M remains unknown. In this study, we determined crystal structures of EGFR T790M or L858R mutants covalently bound by CO-1686. Based on these structural data, we can explain why CO-1686 irreversibly inhibits EGFR and selectively prefers T790M, which may help improving this or similar compounds, and explain why EGFR L718Q and L844V mutations incur resistance to this agent.

  • Organizational Affiliation

    Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor331Homo sapiensMutation(s): 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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 8JC

Download Ideal Coordinates CCD File 
B [auth A]N-[3-[[2-[[4-(4-ethanoylpiperazin-1-yl)-2-methoxy-phenyl]amino]-5-(trifluoromethyl)pyrimidin-4-yl]amino]phenyl]prop-2-enamide
C27 H28 F3 N7 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
8JC BindingDB:  5XDL Ki: min: 74, max: 303 (nM) from 2 assay(s)
Kd: 1.4 (nM) from 1 assay(s)
IC50: min: 0.46, max: 4331 (nM) from 38 assay(s)
EC50: 1655 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.543α = 90
b = 143.543β = 90
c = 143.543γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description