ISDA

Deposition Date 2021-08-23

Release Date 2022-01-19

Last Version Date 2023-10-18

Entry Detail

PDB ID:

7RXR

Keywords:

GENE REGULATION/INHIBITOR

Title:

Crystal Structure of BRD4(D1) with 4-[4-(4-bromophenyl)-1-(piperidin-4-yl)-1H-imidazol-5-yl]-N-(3,5-dimethylphenyl)pyrimidin-2-amine

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.41 Å

R-Value Free:

0.18

R-Value Work:

0.14

R-Value Observed:

0.15

Space Group:

P 21 21 21

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Bromodomain-containing protein 4
Gene (Uniprot):BRD4
Chain IDs:A, B
Chain Length:127
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:O60885 Pfam ID:PF00439

Ligand Molecules

7ZB

EDO

Primary Citation

A Structure-based Design Approach for Generating High Affinity BRD4 D1-Selective Chemical Probes.

Cui, H, Divakaran, A, Hoell, Z.J, Ellingson, M.O, Scholtz, C.R, Zahid, H, Johnson, J.A, Griffith, E.C, Gee, C.T, Lee, A.L, Khanal, S, Shi, K, Aihara, H, Shah, V.H, Lee, R.E, Harki, D.A, Pomerantz, W.C.K.Show

J.Med.Chem. 65 2342 2360 (2022)

PMID: 35007061 DOI: 10.1021/acs.jmedchem.1c01779

Abstact

Chemical probes for epigenetic proteins are essential tools for dissecting the molecular mechanisms for gene regulation and therapeutic development. The bromodomain and extra-terminal (BET) proteins are master transcriptional regulators. Despite promising therapeutic targets, selective small molecule inhibitors for a single bromodomain remain an unmet goal due to their high sequence similarity. Here, we address this challenge via a structure-activity relationship study using 1,4,5-trisubstituted imidazoles against the BRD4 N-terminal bromodomain (D1). Leading compounds 26 and 30 have 15 and 18 nM affinity against BRD4 D1 and over 500-fold selectivity against BRD2 D1 and BRD4 D2 via ITC. Broader BET selectivity was confirmed by fluorescence anisotropy, thermal shift, and CETSA. Despite BRD4 engagement, BRD4 D1 inhibition was unable to reduce c-Myc expression at low concentration in multiple myeloma cells. Conversely, for inflammation, IL-8 and chemokine downregulation were observed. These results provide new design rules for selective inhibitors of an individual BET bromodomain.

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Primary Citation of related structures