7DHS | pdb_00007dhs

Crystal Structure Analysis of the BRD4

• PDB DOI: https://doi.org/10.2210/pdb7DHS/pdb

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


• Deposited: 2020-11-17 Released: 2021-09-15 
• Deposition Author(s): Wu, T., Xiang, Q., Wang, C., Wu, C., Zhang, C., Zhang, M., Liu, Z., Zhang, Y., Xiao, L., Xu, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.253 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Y06014 is a selective BET inhibitor for the treatment of prostate cancer.

Wu, T.B., Xiang, Q.P., Wang, C., Wu, C., Zhang, C., Zhang, M.F., Liu, Z.X., Zhang, Y., Xiao, L.J., Xu, Y.

(2021) Acta Pharmacol Sin 42: 2120-2131

• PubMed: 33654218 
• DOI: https://doi.org/10.1038/s41401-021-00614-7
• Primary Citation Related Structures: 
  7DHS


• PubMed Abstract: 
  

  Bromodomain and extra-terminal proteins (BETs) are potential targets for the therapeutic treatment of prostate cancer (PC). Herein, we report the design, the synthesis, and a structure-activity relationship study of 6-(3,5-dimethylisoxazol-4-yl)benzo[cd]indol-2(1H)-one derivative as novel selective BET inhibitors. One representative compound, 19 (Y06014), bound to BRD4(1) in the low micromolar range and demonstrated high selectivity for BRD4(1) over other non-BET bromodomain-containing proteins. This molecule also potently inhibited cell growth, colony formation, and mRNA expression of AR-regulated genes in PC cell lines. Y06014 also shows stronger activity than the second-generation antiandrogen enzalutamide. Y06014 may serve as a new small molecule probe for further validation of BET as a molecular target for PC drug development.

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Organizational Affiliation: 
• College of Science, Key Laboratory of Rare-earth Chemistry and Applying of Liaoning Province, Shenyang University of Chemical Technology, Shenyang, 110142, China.
Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
College of Pharmacy, Taizhou Polytechnic College, Taizhou, 225300, China.
Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China. [e-mail].
College of Science, Key Laboratory of Rare-earth Chemistry and Applying of Liaoning Province, Shenyang University of Chemical Technology, Shenyang, 110142, China. [e-mail].
Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China. [e-mail].
Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China. [e-mail].
State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.27 kDa 
• Atom Count: 2,233 
• Modeled Residue Count: 252 
• Deposited Residue Count: 282 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A, B	141	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
H8C (Subject of Investigation/LOI)	C [auth A], D [auth B]	6-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(1R)-1-phenylethyl]benzo[cd]indol-2-one C24 H20 N2 O2 ZZRITBGIUCLKNF-OAHLLOKOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.253 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.69	α = 90
b = 78.65	β = 93.49
c = 47.54	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-09-15 
Deposition Author(s): Wu, T., Xiang, Q., Wang, C., Wu, C., Zhang, C., Zhang, M., Liu, Z., Zhang, Y., Xiao, L., Xu, Y.

Revision History  

• Version 1.0: 2021-09-15
  Type: Initial release
  
• Version 1.1: 2022-02-16
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description