8QAR | pdb_00008qar

Crystal Structure of the first bromodomain of BRD4 in complex with acetyl-pyrrole derivative compound 98

• PDB DOI: https://doi.org/10.2210/pdb8QAR/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2023-08-23 Released: 2024-09-11 
• Deposition Author(s): Dalle Vedove, A., Cazzanelli, G., Lolli, G.
• Funding Organization(s): Italian Association for Cancer Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.201 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Enhanced cellular death in liver and breast cancer cells by dual BET/BRPF1 inhibitors.

Cazzanelli, G., Dalle Vedove, A., Sbardellati, N., Valer, L., Caflisch, A., Lolli, G.

(2024) Protein Sci 33: e5191-e5191

• PubMed: 39473021 
• DOI: https://doi.org/10.1002/pro.5191
• Primary Citation Related Structures: 
  8QAL, 8QAN, 8QAP, 8QAR, 8QAZ, 8QB0, 8QB2


• PubMed Abstract: 
  

  The acetylpyrrole scaffold is an acetylated lysine mimic that has been previously explored to develop bromodomain inhibitors. When tested on the hepatoma cell line Huh7 and the breast cancer cell line MDA-MB-231, a few compounds in our acetylpyrrole-thiazole library induced peculiar morphological changes, progressively causing cell death at increasing concentrations. Their evaluation on a panel of human bromodomains revealed concurrent inhibition of BRPF1 and BET bromodomains. To dissect the observed cellular effects, the acetylpyrrole derivatives were compared to JQ1 and GSK6853, chemical probes for the bromodomains of BET and BRPF1, respectively. The appearance of neurite-like extrusions, accompanied by βIII-tubulin overexpression, is caused by BET inhibition, with limited effect on cellular viability. Conversely, interference with BRPF1 induces cellular death but not phenotypic alterations. Combined treatment with JQ1 and GSK6853 showed additivity in reducing cellular viability, comparably to the acetylpyrrole-thiazole-based BET/BRPF1 inhibitors. In addition, we determined the crystallographic structures of the BRD4 and BRPF1 bromodomains in complex with the acetylpyrrole-thiazole compounds. The binding modes in the two bromodomains show similar interactions for the acetylpyrrole and different orientations of the moiety that point to the rim of the acetyl-lysine pocket.

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Organizational Affiliation: 
• Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, Trento, Italy.
Department of Biochemistry, University of Zürich, Zürich, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 15.63 kDa 
• Atom Count: 1,219 
• Modeled Residue Count: 126 
• Deposited Residue Count: 127 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	127	Homo sapiens	Mutation(s): 0  Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
PHAROS:  O60885 GTEx:  ENSG00000141867

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GI0 (Subject of Investigation/LOI)	B [auth A]	3-methyl-1-[2-[4-[(4-methyl-1~{H}-pyrazol-3-yl)methyl]piperazin-1-yl]-1,3-thiazol-4-yl]-2,5,6,7-tetrahydroisoindol-4-one C21 H26 N6 O S NMLXMNVJOHDFQA-UHFFFAOYSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.201 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.32	α = 90
b = 44.38	β = 90
c = 78.415	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-11 
Deposition Author(s): Dalle Vedove, A., Cazzanelli, G., Lolli, G.

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Funding Organization	Location	Grant Number
Italian Association for Cancer Research	Italy	MFAG 2017 - ID. 19882

Revision History  

• Version 1.0: 2024-09-11
  Type: Initial release
  
• Version 1.1: 2025-03-26
  Changes: Database references, Structure summary