3W32 image
Entry Detail
PDB ID:
3W32
Title:
EGFR kinase domain complexed with compound 20a
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2012-12-07
Release Date:
2013-03-06
Method Details:
Experimental Method:
Resolution:
1.80 Å
R-Value Free:
0.23
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Epidermal growth factor receptor
Chain IDs:A
Chain Length:330
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Design and synthesis of novel pyrimido[4,5-b]azepine derivatives as HER2/EGFR dual inhibitors
Bioorg.Med.Chem. 21 2250 2261 (2013)
PMID: 23490150 DOI: 10.1016/j.bmc.2013.02.014

Abstact

A novel 7,6 fused bicyclic scaffold, pyrimido[4,5-b]azepine was designed to fit into the ATP binding site of the HER2/EGFR proteins. The synthesis of this scaffold was accomplished by an intramolecular Claisen-type condensation. As the results of optimization lead us to 4-anilino and 6-functional groups, we discovered 6-substituted amide derivative 19b, which has a 1-benzothiophen-4-yloxy group attached to the 4-anilino group. An X-ray co-crystal structure of 19b with EGFR demonstrated that the N-1 and N-3 nitrogens of the pyrimido[4,5-b]azepine scaffold make hydrogen-bonding interactions with the main chain NH of Met793 and the side chain of Thr854 via a water-mediated hydrogen bond network, respectively. In addition, the NH proton at the 9-position makes an additional hydrogen bond with the carbonyl group of Met793, as we expected. Compound 19b revealed potent HER2/EGFR kinase (IC50: 24/36 nM) and BT474 cell growth (GI50: 18 nM) inhibitory activities based on its pseudo-irreversible (PI) profile.

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Primary Citation of related structures