Structural variation of protein-ligand complexes of the first bromodomain of BRD4

The bromodomain-containing protein 4 (BRD4), a member of the bromodomain and extra-terminal domain (BET) family, plays a key role in several diseases, especially cancers. With increased interest in BRD4 as a therapeutic target, over 300 X-ray crystal structures of the protein in complex with small molecule inhibitors have become publicly available over the recent decade. In this study, we use this structural information to investigate the conformations of the first bromodomain (BD1) of BRD4. Structural alignment shows a high level of similarity between the structures of BRD4-BD1, regardless of the bound ligand. We employ WONKA, a tool for detailed analyses of protein binding sites, to compare the active site of over 100 crystal structures, with a focus on the highly conserved network of water molecules, which line the binding pocket of BRD4-BD1. The analysis presented in this work helps guide the selection of the best structure of BRD4-BD1 to use in structure-based drug design, an important approach for faster and more cost-efficient lead discovery.