Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38.21 kDa 
• Atom Count: 2544 
• Modelled Residue Count: 307 
• Deposited Residue Count: 331 
• Unique protein chains: 1

5XDK

Crystal structure of EGFR 696-1022 T790M in complex with CO-1686

• PDB DOI: 10.2210/pdb5XDK/pdb

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


• Deposited: 2017-03-28 Released: 2017-12-13 
• Deposition Author(s): Yan, X.E., Yun, C.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.248 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

Literature

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

• PubMed: 28881827 
• DOI: 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.

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Organizational Affiliation: 

Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A	331	Homo sapiens	Mutation(s): 1  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8JC	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 HUFOZJXAKZVRNJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
8JC	BindingDB:  5XDK	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

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.248 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.471	α = 90
b = 145.471	β = 90
c = 145.471	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-03-28 
• Released Date: 2017-12-13 
Deposition Author(s): Yan, X.E., Yun, C.H.

Revision History  

• Version 1.0: 2017-12-13
  Type: Initial release