6DMK

A multiconformer ligand model of an isoxazolyl-benzimidazole ligand bound to the bromodomain of human CREBBP

Summary for 6DMK

• Entry DOI: 10.2210/pdb6dmk/pdb
• Descriptor: CREB-binding protein, NITRATE ION, 5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[2-(morpholin-4-yl)ethyl]-2-(2-phenylethyl)-1H-benzimidazole, ... (5 entities in total)
• Functional Keywords: complex, multi conformer model, transcription, transcription-transcription inhibitor complex, transcription/transcription inhibitor
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 1
• Total formula weight: 14103.11

Authors

Hudson, B.M.,van Zundert, G.,Keedy, D.A.,Fonseca, R.,Heliou, A.,Suresh, P.,Borrelli, K.,Day, T.,Fraser, J.S.,van den Bedem, H. (deposition date: 2018-06-05, release date: 2018-12-19, Last modification date: 2024-05-01)

Primary citation

van Zundert, G.C.P.,Hudson, B.M.,de Oliveira, S.H.P.,Keedy, D.A.,Fonseca, R.,Heliou, A.,Suresh, P.,Borrelli, K.,Day, T.,Fraser, J.S.,van den Bedem, H.
qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.
J. Med. Chem., 61:11183-11198, 2018

PubMed Abstract: Proteins and ligands sample a conformational ensemble that governs molecular recognition, activity, and dissociation. In structure-based drug design, access to this conformational ensemble is critical to understand the balance between entropy and enthalpy in lead optimization. However, ligand conformational heterogeneity is currently severely underreported in crystal structures in the Protein Data Bank, owing in part to a lack of automated and unbiased procedures to model an ensemble of protein-ligand states into X-ray data. Here, we designed a computational method, qFit-ligand, to automatically resolve conformationally averaged ligand heterogeneity in crystal structures, and applied it to a large set of protein receptor-ligand complexes. In an analysis of the cancer related BRD4 domain, we found that up to 29% of protein crystal structures bound with drug-like molecules present evidence of unmodeled, averaged, relatively isoenergetic conformations in ligand-receptor interactions. In many retrospective cases, these alternate conformations were adventitiously exploited to guide compound design, resulting in improved potency or selectivity. Combining qFit-ligand with high-throughput screening or multitemperature crystallography could therefore augment the structure-based drug design toolbox.

PubMed: 30457858
DOI: 10.1021/acs.jmedchem.8b01292

Experimental method

X-RAY DIFFRACTION (1.66 Å)