ISDA

Deposition Date 2021-06-27

Release Date 2022-09-21

Last Version Date 2023-10-25

Entry Detail

PDB ID:

7R8R

Keywords:

SIGNALING PROTEIN

Title:

Physachenolide C with Bromodomain (BRD3-BD1)

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.80 Å

R-Value Free:

0.23

R-Value Work:

0.15

R-Value Observed:

0.16

Space Group:

P 2 21 21

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Bromodomain-containing protein 3
Gene (Uniprot):BRD3
Chain IDs:A
Chain Length:121
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q15059 Pfam ID:PF00439

Ligand Molecules

8L6

Primary Citation

Physachenolide C is a Potent, Selective BET Inhibitor.

Zerio, C.J, Sivinski, J, Wijeratne, E.M.K, Xu, Y.M, Ngo, D.T, Ambrose, A.J, Villa-Celis, L, Ghadirian, N, Clarkson, M.W, Zhang, D.D, Horton, N.C, Gunatilaka, A.A.L, Fromme, R, Chapman, E.Show

J.Med.Chem. 66 913 933 (2023)

PMID: 36577036 DOI: 10.1021/acs.jmedchem.2c01770

Abstact

A pulldown using a biotinylated natural product of interest in the 17β-hydroxywithanolide (17-BHW) class, physachenolide C (PCC), identified the bromodomain and extra-terminal domain (BET) family of proteins (BRD2, BRD3, and BRD4), readers of acetyl-lysine modifications and regulators of gene transcription, as potential cellular targets. BROMOscan bromodomain profiling and biochemical assays support PCC as a BET inhibitor with increased selectivity for bromodomain (BD)-1 of BRD3 and BRD4, and X-ray crystallography and NMR studies uncovered specific contacts that underlie the potency and selectivity of PCC toward BRD3-BD1 over BRD3-BD2. PCC also displays characteristics of a molecular glue, facilitating proteasome-mediated degradation of BRD3 and BRD4. Finally, PCC is more potent than other withanolide analogues and gold-standard pan-BET inhibitor (+)-JQ1 in cytotoxicity assays across five prostate cancer (PC) cell lines regardless of androgen receptor (AR)-signaling status.

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Primary Citation of related structures