6UVM

Cocrystal of BRD4(D1) with a methyl carbamate thiazepane inhibitor

Summary for 6UVM

• Entry DOI: 10.2210/pdb6uvm/pdb
• Descriptor: Bromodomain-containing protein 4, 1-[(7S)-7-(thiophen-2-yl)-6,7-dihydro-1,4-thiazepin-4(5H)-yl]ethan-1-one, 1,2-ETHANEDIOL, ... (4 entities in total)
• Functional Keywords: brd4(d1), inhibitor, gene regulation-inhibitor complex, gene regulation/inhibitor
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 1
• Total formula weight: 15400.80

Authors

Johnson, J.A.,Pomerantz, W.C.K. (deposition date: 2019-11-03, release date: 2020-01-01, Last modification date: 2023-10-11)

Primary citation

Johnson, J.A.,Nicolaou, C.A.,Kirberger, S.E.,Pandey, A.K.,Hu, H.,Pomerantz, W.C.K.
Evaluating the Advantages of Using 3D-Enriched Fragments for Targeting BET Bromodomains.
Acs Med.Chem.Lett., 10:1648-1654, 2019

PubMed Abstract: Fragment-based ligand discovery has been successful in targeting diverse proteins. Despite drug-like molecules having more 3D character, traditional fragment libraries are largely composed of flat, aromatic fragments. The use of 3D-enriched fragments for enhancing library diversity is underexplored especially against protein-protein interactions. Here, we evaluate using 3D-enriched fragments against bromodomains. Bromodomains are highly ligandable, but selectivity remains challenging, particularly for bromodomain and extraterminal (BET) family bromodomains. We screened a 3D-enriched fragment library against BRD4(D1) via H CPMG NMR with a protein-observed F NMR secondary assay. The screen led to 29% of the hits that are selective over two related bromodomains, BRDT(D1) and BPTF, and the identification of underrepresented chemical bromodomain inhibitor scaffolds. Initial structure-activity relationship studies guided by X-ray crystallography led to a ligand-efficient thiazepane, with good selectivity and affinity for BET bromodomains. These results suggest that the incorporation of 3D-enriched fragments to increase library diversity can benefit bromodomain screening.

PubMed: 31857841
DOI: 10.1021/acsmedchemlett.9b00414

Experimental method

X-RAY DIFFRACTION (1.51 Å)