Crystal structure of EGFR 696-1022 L858R in complex with SKLB(3)

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Spodoptera frugiperda
  • Mutation(s): Yes 

  • Deposited: 2017-01-31 Released: 2018-02-07 
  • Deposition Author(s): Yun, C.H.
  • Funding Organization(s): National Science Foundation of China, National Basic Research Program of China, Ministry of Science and Technology of China

Experimental Data Snapshot

  • Resolution: 2.95 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Structural insights into drug development strategy targeting EGFR T790M/C797S.

Zhu, S.J.Zhao, P.Yang, J.Ma, R.Yan, X.E.Yang, S.Y.Yang, J.W.Yun, C.H.

(2018) Oncotarget 9: 13652-13665

  • DOI: https://doi.org/10.18632/oncotarget.24113
  • Primary Citation of Related Structures:  
    5X26, 5X27, 5X28, 5X2A, 5X2C, 5X2F, 5X2K

  • PubMed Abstract: 

    Treatment of non-small-cell lung cancers (NSCLCs) harboring primary EGFR oncogenic mutations such as L858R and exon 19 deletion delE746_A750 (Del-19) using gefitinib/erlotinib ultimately fails due to the emergence of T790M mutation. Though WZ4002/CO-1686/AZD9291 are effective in overcoming EGFR T790M by targeting Cys797 via covalent bonding, their efficacy is again limited due to the emergence of C797S mutation. New agents effectively inhibiting EGFR T790M without covalent linkage through Cys 797 may solve this problem. We presented here crystal structures of EGFR activating/drug-resistant mutants in complex with a panel of reversible inhibitors along with mutagenesis and enzyme kinetic data. These data revealed a previously un-described hydrophobic clamp structure in the EGFR kinase which may be exploited to facilitate development of next generation drugs targeting EGFR T790M with or without concomitant C797S. Interestingly, mutations in the hydrophobic clamp that hinder drug binding often also weaken ATP binding and/or abolish kinase activity, thus do not readily result in resistance to the drugs.

  • 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 receptor327Homo 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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 7XO

Download Ideal Coordinates CCD File 
B [auth A]N2-[4-(4-methylpiperazin-1-yl)phenyl]-N8-phenyl-9-propan-2-yl-purine-2,8-diamine
C25 H30 N8
Query on CL

Download Ideal Coordinates CCD File 
Binding Affinity Annotations 
IDSourceBinding Affinity
7XO BindingDB:  5X26 IC50: min: 5, max: 46 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.95 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.278α = 90
b = 145.278β = 90
c = 145.278γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

  • Released Date: 2018-02-07 
  • Deposition Author(s): Yun, C.H.

Funding OrganizationLocationGrant Number
National Science Foundation of ChinaChina31270769
National Basic Research Program of ChinaChina2012CB917202
Ministry of Science and Technology of ChinaChinaNCET-12-0013

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references
  • Version 1.2: 2018-04-11
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description