8WYP

High Resolution Crystal Structure of Brd4 BD-1 in Complex with a Novel Inhibitor Precursor

• PDB DOI: https://doi.org/10.2210/pdb8WYP/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-10-31 Released: 2024-05-22 
• Deposition Author(s): Liu, B., Ma, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free: 0.214 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

High resolution crystal structure of BRD4-BD1 in complex with a novel inhibitor precursor.

Ma, X., Wang, M., Wang, F., Li, J., Zhang, Z., Zhu, J., Liu, B.

(2024) Biochem Biophys Res Commun 690: 149284-149284

• PubMed: 38006801 
• DOI: https://doi.org/10.1016/j.bbrc.2023.149284
• Primary Citation of Related Structures:  
  8WYP


• PubMed Abstract: 
  

  The inhibition of BRD4 bromodomain is an effective therapeutic strategy for a variety of diseases in which BRD4 are implicated. Herein, we identified a small-molecule BRD4 inhibitor hit named compound 3 using high-throughput screening. The 1.6 Å resolution co-crystal structure confirmed that the compound occupies the KAc recognition pockets of BRD4 by forming key hydrogen bonds with Asn140 and engaging in hydrophobic interactions, thus impedes the binding of acetylated lysine to BRD4. These findings suggest compound 3 can be a lead compound to develop a structurally novel BRD4 inhibitors.

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Organizational Affiliation: 

School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 15.31 kDa 
• Atom Count: 1,250 
• Modelled Residue Count: 125 
• Deposited Residue Count: 125 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	125	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XUK (Subject of Investigation/LOI)	B [auth A], C [auth A]	3-bromanylimidazo[1,2-a]pyridin-6-amine C7 H6 Br N3 PTBAMOLKKZXWMQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free: 0.214 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.32	α = 90
b = 47.32	β = 90
c = 78.76	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-22 
Deposition Author(s): Liu, B., Ma, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-05-22
  Type: Initial release