Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39039.29 
• Atom Count: 2582 
• Residue Count: 330 
• Unique protein chains: 1

4G5J

Crystal structure of EGFR kinase in complex with BIBW2992

• DOI: 10.2210/pdb4G5J/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens


• Deposited: 2012-07-18 Released: 2012-08-29 
• Deposition Author(s): Solca, F., Dahl, G., Zoephel, A., Bader, G., Sanderson, M., Klein, C., Kraemer, O., Himmelsbach, F., Haaksma, E., Adolf, G.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.259 
• R-Value Work: 0.205 

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

• PubMed: 22888144 
• DOI: 10.1124/jpet.112.197756
• Primary Citation of Related Structures:  
  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-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."

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Organizational Affiliation: 

Boehringer Ingelheim RCV GmbH & Co. KG., Vienna, Austria. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Epidermal growth factor receptor	A	330	Homo sapiens	Mutation(s): 0  Gene Names: EGFR (ERBB, ERBB1, HER1) EC: 2.7.10.1
Find proteins for P00533 (Homo sapiens) Go to Gene View: EGFR Go to UniProtKB:  P00533

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
0WN	A	N-{4-[(3-chloro-4-fluorophenyl)amino]-7-[(3S)-tetrahydrofuran-3-yloxy]quinazolin-6-yl}-4-(dimethylamino)butanamide Afatinib, bound form C24 H27 Cl F N5 O3 JSENTLOBWVHLNR-INIZCTEOSA-N
0WM	A	(2E)-N-{4-[(3-chloro-4-fluorophenyl)amino]-7-[(3S)-tetrahydrofuran-3-yloxy]quinazolin-6-yl}-4-(dimethylamino)but-2-enamide Afatinib C24 H25 Cl F N5 O3 ULXXDDBFHOBEHA-CWDCEQMOSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
0WM	Kd: 0.1 - 1.1 nM (100) BINDINGDB
0WM	IC50: 0.2 - 47 nM (100) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.259 
• R-Value Work: 0.205 
• Space Group: I 2 3

Unit Cell:

Length (Å)	Angle (°)
a = 144.468	α = 90.00
b = 144.468	β = 90.00
c = 144.468	γ = 90.00

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-07-18 
• Released Date: 2012-08-29 
• Deposition Author(s): Solca, F., Dahl, G., Zoephel, A., Bader, G., Sanderson, M., Klein, C., Kraemer, O., Himmelsbach, F., Haaksma, E., Adolf, G.R.

Revision History 

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