2J5F

Crystal structure of EGFR kinase domain in complex with an irreversible inhibitor 34-jab

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structure-Guided Development of Affinity Probes for Tyrosine Kinases Using Chemical Genetics.

Blair, J.A., Rauh, D., Kung, C., Yun, C.-H., Fan, Q.-W., Rode, H., Zhang, C., Eck, M.J., Weiss, W.A., Shokat, K.M.

(2007) Nat Chem Biol 3: 229

  • DOI: 10.1038/nchembio866
  • Primary Citation of Related Structures:  
    2HWP, 2HWO, 2J5F, 2J5E

  • PubMed Abstract: 

    • As key components in nearly every signal transduction pathway, protein kinases are attractive targets for the regulation of cellular signaling by small-molecule inhibitors. We report the structure-guided development of 6-acrylamido-4-anilinoquinazoline irreversible kinase inhibitors that potently and selectively target rationally designed kinases bearing two selectivity elements that are not found together in any wild-type kinase: an electrophile-targeted cysteine residue and a glycine gatekeeper residue ...

    As key components in nearly every signal transduction pathway, protein kinases are attractive targets for the regulation of cellular signaling by small-molecule inhibitors. We report the structure-guided development of 6-acrylamido-4-anilinoquinazoline irreversible kinase inhibitors that potently and selectively target rationally designed kinases bearing two selectivity elements that are not found together in any wild-type kinase: an electrophile-targeted cysteine residue and a glycine gatekeeper residue. Cocrystal structures of two irreversible quinazoline inhibitors bound to either epidermal growth factor receptor (EGFR) or engineered c-Src show covalent inhibitor binding to the targeted cysteine (Cys797 in EGFR and Cys345 in engineered c-Src). To accommodate the new covalent bond, the quinazoline core adopts positions that are different from those seen in kinase structures with reversible quinazoline inhibitors. Based on these structures, we developed a fluorescent 6-acrylamido-4-anilinoquinazoline affinity probe to report the fraction of kinase necessary for cellular signaling, and we used these reagents to quantitate the relationship between EGFR stimulation by EGF and its downstream outputs-Akt, Erk1 and Erk2.

    Organizational Affiliation: 

    Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EPIDERMAL GROWTH FACTOR RECEPTOR A327Homo sapiensMutation(s): 0 
Gene Names: EGFR, ERBB, ERBB1, 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
DJK
Query on DJK
Download Ideal Coordinates CCD File 
A
N-[4-(3-BROMO-PHENYLAMINO)-QUINAZOLIN-6-YL]-ACRYLAMIDE
C17 H13 Br N4 O
HTUBKQUPEREOGA-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DJKIC50:  1.690000057220459   nM  BindingDB
DJKIC50:  4.300000190734863   nM  BindingDB
DJKIC50:  2   nM  BindingDB
DJKIC50:  3.9000000953674316   nM  BindingDB
DJKIC50:  130   nM  BindingDB
DJKIC50:  521   nM  BindingDB
DJKIC50:  0.699999988079071   nM  BindingDB
DJKIC50:  12   nM  BindingDB
DJKIC50:  36   nM  BindingDB
DJKIC50:  152   nM  BindingDB
DJKIC50:  1.2000000476837158   nM  BindingDB
DJKIC50:  2.700000047683716   nM  BindingDB
DJKIC50:  18   nM  BindingDB
DJKIC50:  0.07999999821186066   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.194 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.876α = 90
b = 145.876β = 90
c = 145.876γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2006-09-14 
  • Released Date: 2007-02-27 
    • Deposition Author(s): Yun, C.-H., Eck, M.J.

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-27
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance