4G5J

Crystal structure of EGFR kinase in complex with BIBW2992

DOI: 10.2210/pdb4G5J/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Mutation(s): No

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.

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

PubMed: 22888144 Search on PubMed
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-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
Molecule	Chains	Sequence Length	Organism	Details	Image
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) Explore P00533 Go to UniProtKB: P00533
NIH Common Fund Data Resources
PHAROS: P00533 GTEx: ENSG00000146648
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0WN Query on 0WN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth 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 Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth 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
ID	Binding Affinity (Sequence Identity %)
0WM	IC50: 1 nM BindingDB
0WM	IC50: 0.5699999928474426 nM BindingDB
0WM	IC50: 3.799999952316284 nM BindingDB
0WM	Kd: 0.14000000059604645 nM BindingDB
0WM	IC50: 11 nM BindingDB
0WM	IC50: 12 nM BindingDB
0WM	Kd: 0.23000000417232513 nM BindingDB
0WM	Kd: 0.11999999731779099 nM BindingDB
0WM	IC50: 0.9700000286102295 nM BindingDB
0WM	IC50: 0.1899999976158142 nM BindingDB
0WM	Kd: 0.10999999940395355 nM BindingDB
0WM	Kd: 0.6100000143051147 nM BindingDB
0WM	IC50: 0.9599999785423279 nM BindingDB
0WM	IC50: 0.4000000059604645 nM BindingDB
0WM	IC50: 23 nM BindingDB
0WM	Kd: 1.100000023841858 nM BindingDB
0WM	Kd: 0.25 nM BindingDB
0WM	Kd: 0.1899999976158142 nM BindingDB
0WM	Kd: 0.10000000149011612 nM BindingDB
0WM	IC50: 1 nM BindingDB
0WM	IC50: 0.5 nM BindingDB
0WM	IC50: 47 nM BindingDB
0WM	IC50: 1.600000023841858 nM BindingDB
0WM	IC50: 10 nM BindingDB
0WM	Kd: 0.20000000298023224 nM BindingDB
0WM	IC50: 5 nM BindingDB