5Z1S

Crystal Structure Analysis of the BRD4(1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Y08060: A Selective BET Inhibitor for Treatment of Prostate Cancer.

Xiang, Q.Zhang, Y.Li, J.Xue, X.Wang, C.Song, M.Zhang, C.Wang, R.Li, C.Wu, C.Zhou, Y.Yang, X.Li, G.Ding, K.Xu, Y.

(2018) Acs Med.Chem.Lett. 9: 262-267

  • DOI: 10.1021/acsmedchemlett.8b00003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Prostate cancer is a commonly diagnosed cancer and a leading cause of cancer-related deaths. The bromodomain and extra terminal domain (BET) family proteins have emerged as potential therapeutic targets for the treatment of castration-resistant prost ...

    Prostate cancer is a commonly diagnosed cancer and a leading cause of cancer-related deaths. The bromodomain and extra terminal domain (BET) family proteins have emerged as potential therapeutic targets for the treatment of castration-resistant prostate cancer. A series of 2,2-dimethyl-2 H -benzo[ b ][1,4]oxazin-3(4 H )-one derivatives were designed and synthesized as selective bromodomain containing protein 4 (BRD4) inhibitors. The compounds potently inhibit BRD4(1) with nanomolar IC 50 values and exhibit high selectivity over most non-BET subfamily members. One of the representative compounds 36 (Y08060) effectively suppresses cell growth, colony formation, and expression of androgen receptor (AR), AR regulated genes, and MYC in prostate cancer cell lines. In in vivo studies, 36 demonstrates a good PK profile with high oral bioavailability (61.54%) and is a promising lead compound for further prostate cancer drug development.


    Organizational Affiliation

    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, China.,Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, The Chinese Academy of Sciences, Dalian, Liaoning 116023, China.,School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China.,University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China.,School of Pharmaceutical Sciences, Jilin University, No. 1266 Fujin Road, Chaoyang District, Changchun, Jilin 130021, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bromodomain-containing protein 4
A
141Homo 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EFM
Query on EFM

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Download CCD File 
A
5-bromo-2-methoxy-N-(6-methoxy-2,2-dimethyl-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-7-yl)benzene-1-sulfonamide
C18 H19 Br N2 O6 S
BVPMJOFBUGYDAV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download SDF File 
Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 35.080α = 90.00
b = 47.090β = 90.00
c = 78.170γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-02
    Type: Initial release
  • Version 1.1: 2019-07-24
    Type: Data collection, Database references