5Z5U

The first bromodomain of BRD4 with compound BDF-2254


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.631 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Development and evaluation of a novel series of Nitroxoline-derived BET inhibitors with antitumor activity in renal cell carcinoma.

Chen, W.Zhang, H.Chen, Z.Jiang, H.Liao, L.Fan, S.Xing, J.Xie, Y.Chen, S.Ding, H.Chen, K.Jiang, H.Luo, C.Zheng, M.Yao, Z.Huang, Y.Zhang, Y.

(2018) Oncogenesis 7: 83-83

  • DOI: 10.1038/s41389-018-0093-z
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Small molecular inhibitors targeting BRD4 family proteins are emerging as promising therapies in many types of human malignancies. However, whether BRD4, as well as other BET family members, may serve as therapeutic targets in renal cell carcinoma (R ...

    Small molecular inhibitors targeting BRD4 family proteins are emerging as promising therapies in many types of human malignancies. However, whether BRD4, as well as other BET family members, may serve as therapeutic targets in renal cell carcinoma (RCC) remains unknown. In this study, we found that both BRD2 and BRD4 were over-expressed in RCC tissues, knock-down both of which achieved potent anti-proliferative effects in RCC cells. A novel category of BET inhibitors, originated from an approved drug Nitroxoline, were synthesized and evaluated with biochemical and cellular assays, as well as the method of crystallography. The complex crystal structures of several compounds in this category with the first bromodomain of BRD4 (BRD4-BD1) were solved, revealing the binding mechanism and facilitating further structural optimizations. Among them, compound BDF-1253 showed an approximately four-fold improvement in BRD4 inhibition compared with the prototype Nitroxoline and had good selectivity for BET proteins against other bromodomain proteins or epi-enzymes in biochemical assays. Compound BDF-1253 efficiently suppressed the expression of BET downstream genes, impaired RCC cells viability via inducing cell cycle arrest and apoptosis, and decreased tumor growth in RCC xenografts. In summary, these results suggest that inhibition of BET family members has great therapeutic potentials in the treatment of RCC, and the novel series of BET inhibitors reported here are promising to become RCC drug candidates.


    Organizational Affiliation

    Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.,University of Chinese Academy of Sciences, Beijing, 100049, China. zhangyy@simm.ac.cn.,Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,College of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, 210032, China.,Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China. myzheng@simm.ac.cn.,University of Chinese Academy of Sciences, Beijing, 100049, China. myzheng@simm.ac.cn.,School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.,Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China. hyrrenji2@aliyun.com.,Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China. zhangyy@simm.ac.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bromodomain-containing protein 4
A
125Homo sapiensMutation(s): 0 
Gene Names: BRD4 (HUNK1)
Find proteins for O60885 (Homo sapiens)
Go to Gene View: BRD4
Go to UniProtKB:  O60885
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
96U
Query on 96U

Download SDF File 
Download CCD File 
A
2-amino-4-(1H-imidazol-1-yl)quinoline-6,8-diol
C12 H10 N4 O2
ORPCIQGKZXBLNN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.631 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 32.006α = 90.00
b = 47.276β = 90.00
c = 78.794γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-01-20 
  • Released Date: 2019-01-23 
  • Deposition Author(s): Zhang, H., Luo, C.

Revision History 

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-03-06
    Type: Data collection, Database references