4G5J

Crystal structure of EGFR kinase in complex with BIBW2992


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Target Binding Properties and Cellular Activity of Afatinib (BIBW 2992), an Irreversible ErbB Family Blocker.

Solca, F.Dahl, G.Zoephel, A.Bader, G.Sanderson, M.Klein, C.Kraemer, O.Himmelsbach, F.Haaksma, E.Adolf, G.R.

(2012) J Pharmacol Exp Ther 343: 342-350

  • DOI: 10.1124/jpet.112.197756
  • Primary Citation of Related Structures:  
    4G5J, 4G5P

  • PubMed Abstract: 
  • Deregulation of the ErbB (proto-oncogene B of the avian erythroblastosis virus AEV-H strain) receptor network is well recognized as an oncogenic driver in epithelial cancers. Several targeted drugs have been developed, including antibodies and small- ...

    Deregulation of the ErbB (proto-oncogene B of the avian erythroblastosis virus AEV-H strain) receptor network is well recognized as an oncogenic driver in epithelial cancers. Several targeted drugs have been developed, including antibodies and small-molecule kinase inhibitors, each of them characterized by distinct patterns of ErbB receptor interactions. Understanding the precise pharmacological properties of these compounds is important for optimal use in clinical practice. Afatinib [BIBW 2992; N-[4-[(3-chloro-4-fluorophenyl)amino]-7-[[(3S)-tetrahydro-3-furanyl]oxy]-6-quinazolinyl]-4-(dimethylamino)-2-butenamide] is an ATP-competitive anilinoquinazoline derivative harboring a reactive acrylamide group. It was designed to covalently bind and irreversibly block enzymatically active ErbB receptor family members. Here, we show by X-ray crystallography the covalent binding of afatinib to wild-type epidermal growth factor receptor (EGFR) and by mass spectrometry the covalent interaction with EGFR, EGFRL858R/T790M, human epidermal growth factor receptor 2 (HER2), and ErbB-4. Afatinib potently inhibits the enymatic activity of ErbB-4 (EC50=1 nM) and the proliferation of cancer cell lines driven by multiple ErbB receptor aberrations at concentrations below 100 nM. N-[4-[(3-chloro-4-fluorophenyl)amino]-7-[[(3S)-tetrahydro-3-furanyl]oxy]-6-quinazolinyl]-4-(dimethylamino)-2-butanamide (BI 37781), a close analog of afatinib lacking the acrylamide group and thus incapable of covalent bond formation, had similar potency on cells driven by EGFR or EGFRL858R, but less or no detectable activity on cells expressing EGFRL858R/T790M HER2 or ErbB-4. These results stress the importance of the acrylamide group and show that afatinib differs from approved ErbB targeting agents by irreversibly inhibiting the kinase activity of all ErbB family members. They provide a mechanistic rationale for the distinct pharmacological features of this compound and explain the clinical activity seen in some patients who are resistant to antibody or kinase inhibitor therapy because of secondary mutations or ErbB receptor "reprogramming."


    Organizational Affiliation

    Boehringer Ingelheim RCV GmbH & Co. KG., Vienna, Austria. flavio.solca@boehringer-ingelheim.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Epidermal growth factor receptorA330Homo sapiensMutation(s): 0 
Gene Names: EGFRERBBERBB1HER1
EC: 2.7.10.1
Find proteins for P00533 (Homo sapiens)
Explore P00533 
Go to UniProtKB:  P00533
NIH Common Fund Data Resources
PHAROS  P00533
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0WN
Query on 0WN

Download CCD File 
A
N-{4-[(3-chloro-4-fluorophenyl)amino]-7-[(3S)-tetrahydrofuran-3-yloxy]quinazolin-6-yl}-4-(dimethylamino)butanamide
C24 H27 Cl F N5 O3
JSENTLOBWVHLNR-INIZCTEOSA-N
 Ligand Interaction
0WM
Query on 0WM

Download CCD File 
A
(2E)-N-{4-[(3-chloro-4-fluorophenyl)amino]-7-[(3S)-tetrahydrofuran-3-yloxy]quinazolin-6-yl}-4-(dimethylamino)but-2-enamide
C24 H25 Cl F N5 O3
ULXXDDBFHOBEHA-CWDCEQMOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0WMIC50:  1   nM  BindingDB
0WMKd:  1.100000023841858   nM  BindingDB
0WMKd:  0.14000000059604645   nM  BindingDB
0WMKd:  0.25   nM  BindingDB
0WMIC50:  11   nM  BindingDB
0WMKd:  0.1899999976158142   nM  BindingDB
0WMKd:  0.10000000149011612   nM  BindingDB
0WMKd:  0.23000000417232513   nM  BindingDB
0WMKd:  0.11999999731779099   nM  BindingDB
0WMIC50:  0.9700000286102295   nM  BindingDB
0WMIC50:  0.1899999976158142   nM  BindingDB
0WMIC50:  1   nM  BindingDB
0WMKd:  0.10999999940395355   nM  BindingDB
0WMKd:  0.6100000143051147   nM  BindingDB
0WMIC50:  0.5   nM  BindingDB
0WMIC50:  0.9599999785423279   nM  BindingDB
0WMIC50:  47   nM  BindingDB
0WMIC50:  1.600000023841858   nM  BindingDB
0WMKd:  0.20000000298023224   nM  BindingDB
0WMIC50:  5   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.468α = 90
b = 144.468β = 90
c = 144.468γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2012-10-31
    Changes: Database references