3IKA

Crystal Structure of EGFR 696-1022 T790M Mutant Covalently Binding to WZ4002

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Novel mutant-selective EGFR kinase inhibitors against EGFR T790M.

Zhou, W., Ercan, D., Chen, L., Yun, C.H., Li, D., Capelletti, M., Cortot, A.B., Chirieac, L., Iacob, R.E., Padera, R., Engen, J.R., Wong, K.K., Eck, M.J., Gray, N.S., Janne, P.A.

(2009) Nature 462: 1070-1074

  • DOI: 10.1038/nature08622
  • Primary Citation of Related Structures:  
    3IKA

  • PubMed Abstract: 

    • The clinical efficacy of epidermal growth factor receptor (EGFR) kinase inhibitors in EGFR-mutant non-small-cell lung cancer (NSCLC) is limited by the development of drug-resistance mutations, including the gatekeeper T790M mutation. Strategies targeting ...

    The clinical efficacy of epidermal growth factor receptor (EGFR) kinase inhibitors in EGFR-mutant non-small-cell lung cancer (NSCLC) is limited by the development of drug-resistance mutations, including the gatekeeper T790M mutation. Strategies targeting EGFR T790M with irreversible inhibitors have had limited success and are associated with toxicity due to concurrent inhibition of wild-type EGFR. All current EGFR inhibitors possess a structurally related quinazoline-based core scaffold and were identified as ATP-competitive inhibitors of wild-type EGFR. Here we identify a covalent pyrimidine EGFR inhibitor by screening an irreversible kinase inhibitor library specifically against EGFR T790M. These agents are 30- to 100-fold more potent against EGFR T790M, and up to 100-fold less potent against wild-type EGFR, than quinazoline-based EGFR inhibitors in vitro. They are also effective in murine models of lung cancer driven by EGFR T790M. Co-crystallization studies reveal a structural basis for the increased potency and mutant selectivity of these agents. These mutant-selective irreversible EGFR kinase inhibitors may be clinically more effective and better tolerated than quinazoline-based inhibitors. Our findings demonstrate that functional pharmacological screens against clinically important mutant kinases represent a powerful strategy to identify new classes of mutant-selective kinase inhibitors.

    Organizational Affiliation: 

    Department of Cancer Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Epidermal growth factor receptor A, B331Homo sapiensMutation(s): 1 
Gene Names: EGFR, ERBB1, ERBB, HER1
EC: 2.7.10.1
Find proteins for P00533 (Homo sapiens)
Explore P00533 
Go to UniProtKB:  P00533
NIH Common Fund Data Resources
PHAROS:  P00533
GTEx:  ENSG00000146648
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0UN
Query on 0UN
Download Ideal Coordinates CCD File 
A
N-{3-[(5-chloro-2-{[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)oxy]phenyl}prop-2-enamide
C25 H27 Cl N6 O3
ITTRLTNMFYIYPA-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0UNIC50:  0.6600000262260437   nM  BindingDB
0UNIC50:  3.200000047683716   nM  BindingDB
0UNIC50:  18   nM  BindingDB
0UNIC50:  16   nM  BindingDB
0UNIC50:  11   nM  BindingDB
0UNIC50:  10   nM  BindingDB
0UNIC50:  4.400000095367432   nM  BindingDB
0UNIC50:  1   nM  BindingDB
0UNIC50:  9.699999809265137   nM  BindingDB
0UNIC50:  110   nM  BindingDB
0UNIC50:  2.5999999046325684   nM  BindingDB
0UNIC50:  1.0199999809265137   nM  BindingDB
0UNIC50 :  14   nM  PDBBind
0UNIC50:  79   nM  BindingDB
0UNIC50:  2.200000047683716   nM  BindingDB
0UNIC50:  9.579999923706055   nM  BindingDB
0UNIC50:  1.399999976158142   nM  BindingDB
0UNIC50:  0.800000011920929   nM  BindingDB
0UNIC50:  1180   nM  BindingDB
0UNIC50:  0.41999998688697815   nM  BindingDB
0UNIC50:  44   nM  BindingDB
0UNIC50:  710   nM  BindingDB
0UNIC50:  6.179999828338623   nM  BindingDB
0UNIC50:  46   nM  BindingDB
0UNIC50:  3   nM  BindingDB
0UNIC50:  0.1899999976158142   nM  BindingDB
0UNIC50:  5.400000095367432   nM  BindingDB
0UNKd:  46   nM  BindingDB
0UNIC50:  31   nM  BindingDB
0UNIC50:  3.799999952316284   nM  BindingDB
0UNIC50:  23   nM  BindingDB
0UNKd:  12   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.23α = 90
b = 89.126β = 90
c = 165.224γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2009-08-05 
  • Released Date: 2010-01-12 
    • Deposition Author(s): Yun, C.-H., Eck, M.J.

Revision History 

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance