ISDA

Entry Detail

PDB ID:

5II2

Keywords:

Title:

Crystal Structure of the fifth bromodomain of human polybromo (PB1) in complex with 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one

Biological Source:

Source Organism:

Homo sapiens

Host Organism:

Escherichia coli BL21(DE3)

PDB Version:

Deposition Date:

2016-03-01

Release Date:

2016-06-29

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.10 Å

R-Value Free:

0.22

R-Value Work:

0.17

R-Value Observed:

0.17

Space Group:

P 21 21 21

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:Protein polybromo-1
Chain IDs:A, B
Chain Length:124
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:Q86U86 Pfam ID:PF00439

Ligand Molecules

CIT

LU2

Primary Citation

Discovery and Optimization of a Selective Ligand for the Switch/Sucrose Nonfermenting-Related Bromodomains of Polybromo Protein-1 by the Use of Virtual Screening and Hydration Analysis.

Myrianthopoulos, V, Gaboriaud-Kolar, N, Tallant, C, Hall, M.L, Grigoriou, S, Brownlee, P.M, Fedorov, O, Rogers, C, Heidenreich, D, Wanior, M, Drosos, N, Mexia, N, Savitsky, P, Bagratuni, T, Kastritis, E, Terpos, E, Filippakopoulos, P, Muller, S, Skaltsounis, A.L, Downs, J.A, Knapp, S, Mikros, E.Show

J.Med.Chem. 59 8787 8803 (2016)

PMID: 27617704 DOI: 10.1021/acs.jmedchem.6b00355

Abstact

Bromodomains (BRDs) are epigenetic interaction domains currently recognized as emerging drug targets for development of anticancer or anti-inflammatory agents. In this study, development of a selective ligand of the fifth BRD of polybromo protein-1 (PB1(5)) related to switch/sucrose nonfermenting (SWI/SNF) chromatin remodeling complexes is presented. A compound collection was evaluated by consensus virtual screening and a hit was identified. The biophysical study of protein-ligand interactions was performed using X-ray crystallography and isothermal titration calorimetry. Collective data supported the hypothesis that affinity improvement could be achieved by enhancing interactions of the complex with the solvent. The derived SAR along with free energy calculations and a consensus hydration analysis using WaterMap and SZmap algorithms guided rational design of a set of novel analogues. The most potent analogue demonstrated high affinity of 3.3 μM and an excellent selectivity profile, thus comprising a promising lead for the development of chemical probes targeting PB1(5).

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Primary Citation of related structures