5H21 | pdb_00005h21

Trimethoxy-ring inhibitor in complex with the first bromodomain of BRD4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 
    0.190 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.162 (Depositor) 
  • R-Value Observed: 
    0.163 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5H21

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of novel trimethoxy-ring BRD4 bromodomain inhibitors: AlphaScreen assay, crystallography and cell-based assay.

Chen, Z.Zhang, H.Liu, S.Xie, Y.Jiang, H.Lu, W.Xu, H.Yue, L.Zhang, Y.Ding, H.Zheng, M.Yu, K.Chen, K.Jiang, H.Luo, C.

(2017) Medchemcomm 8: 1322-1331

  • DOI: https://doi.org/10.1039/c7md00083a
  • Primary Citation Related Structures: 
    5H21

  • PubMed Abstract: 

    As a member of the bromodomain and extra terminal domain (BET) protein family, BRD4 is closely related to cancers and other diseases. Small-molecule BRD4 inhibitors have already demonstrated promising potential for the therapy of BRD4-related cancers. In this study, we report the discovery and evaluation of a novel category of BRD4 inhibitors, which share a trimethoxy ring and target the first bromodomain of the human BRD4 protein. The IC 50 value of the most potent compound, DC-BD-03, is 2.01 μM. In addition, a high-resolution crystal structure of the compound DC-BD-29 with the first bromodomain of BRD4 was determined, which revealed the binding mode and facilitated further structure-based optimization. These compounds exhibited anti-proliferation activity, caused cell cycle arrest, and induced apoptosis in human leukemia MV4-11 cells. Thus, the results presented in this study indicated the potential of this series of compounds as drug candidates for the therapy of BRD4-related cancers.


  • Organizational Affiliation
    • Drug Discovery and Design Center , State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China . Email: 10110700070@fudan.edu.cn ; Email: hding@simm.ac.cn ; Email: cluo@simm.ac.cn ; Tel: +86 21 50806600.

Macromolecule Content 

  • Total Structure Weight: 17.02 kDa 
  • Atom Count: 1,216 
  • Modeled Residue Count: 124 
  • Deposited Residue Count: 139 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4139Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
PHAROS:  O60885
GTEx:  ENSG00000141867 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RMR

Query on RMR



Download:Ideal Coordinates CCD File
B [auth A]3,4,5-trimethoxy-~{N}-(2-thiophen-2-ylethyl)benzamide
C16 H19 N O4 S
SKGBFUKYQVAIFX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free:  0.190 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.162 (Depositor) 
  • R-Value Observed: 0.163 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.322α = 90
b = 47.291β = 90
c = 79.466γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references