8WYG | pdb_00008wyg

Crystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor 22

• PDB DOI: https://doi.org/10.2210/pdb8WYG/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-10-30 Released: 2024-01-24 
• Deposition Author(s): Xu, H., Zhao, X., Shen, H., Xu, Y., Wu, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.13 Å
• R-Value Free: 
  0.257 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.195 (Depositor) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Discovery of Novel Phenoxyaryl Pyridones as Bromodomain and Extra-Terminal Domain (BET) Inhibitors with High Selectivity for the Second Bromodomain (BD2) to Potentially Treat Acute Myeloid Leukemia.

Jiang, W., Hou, Q., Xu, H., Yang, K., Wang, X., Zhang, K., Zeng, Y., Li, W., Wang, B., Luo, G., Zhao, X., Shen, H., Xu, Y., Wu, X.

(2024) J Med Chem 67: 1513-1532

• PubMed: 38175809 
• DOI: https://doi.org/10.1021/acs.jmedchem.3c02104
• Primary Citation Related Structures: 
  8WXY, 8WY3, 8WY7, 8WYG


• PubMed Abstract: 
  

  Bromodomain-selective BET inhibition has emerged as a promising strategy to improve the safety profiles of pan -BET inhibitors. Herein, we report the discovery of potent phenoxyaryl pyridones as highly BD2-selective BET inhibitors. Compound 23 (IC ₅₀ = 2.9 nM) exhibited a comparable BRD4 BD2 inhibitory activity relative to 10 (IC ₅₀ = 1.0 nM) and remarkably improved selectivity over BRD4 BD1 ( 23 : 2583-fold; 10 : 344-fold). This lead compound significantly inhibited the proliferation of acute myeloid leukemia (AML) cell lines through induction of G0/G1 arrest and apoptosis in vitro . Excellent in vivo antitumor efficacy with 23 was achieved in an MV;411 mouse xenograft model. Pleasingly, compound 23 (hERG IC ₅₀ > 30 μM) mitigated the inhibition of the human ether-à-go-go-related gene (hERG) ion channel compared with 10 (hERG IC ₅₀ = 2.8 μM). This work provides a promising BD2-selective lead for the development of more effective and safe BET inhibitors as anticancer agents.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China.
Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 511436, China.
China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, 510530, China.
State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 66.13 kDa 
• Atom Count: 3,792 
• Modeled Residue Count: 439 
• Deposited Residue Count: 544 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 2	A, B, C, D	136	Homo sapiens	Mutation(s): 0  Gene Names: BRD2, KIAA9001, RING3
UniProt & NIH Common Fund Data Resources
Find proteins for P25440 (Homo sapiens) Explore P25440  Go to UniProtKB:  P25440
PHAROS:  P25440 GTEx:  ENSG00000204256

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XHN (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	2-[[5-[2-(4-fluoranyl-2,6-dimethyl-phenoxy)-5-(2-oxidanylpropan-2-yl)phenyl]-1-methyl-2-oxidanylidene-pyridin-4-yl]amino]-~{N}-(4-oxidanylcyclohexyl)ethanamide C31 H38 F N3 O5 AYFFWGHTVVFMSI-YHBQERECSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.13 Å
• R-Value Free:  0.257 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.195 (Depositor) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.782	α = 90
b = 95.497	β = 90
c = 109.08	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-01-24 
Deposition Author(s): Xu, H., Zhao, X., Shen, H., Xu, Y., Wu, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22307116

Revision History  

• Version 1.0: 2024-01-24
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Database references, Refinement description