5WUU

Complex structure of the first bromodomain of BRD4 with an inhibitor that containing a 2H-chromen-2-one ring


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of novel BRD4 inhibitors by high-throughput screening, crystallography, and cell-based assays.

Sun, Z.Zhang, H.Chen, Z.Xie, Y.Jiang, H.Chen, L.Ding, H.Zhang, Y.Jiang, H.Zheng, M.Luo, C.

(2017) Bioorg Med Chem Lett 27: 2003-2009

  • DOI: https://doi.org/10.1016/j.bmcl.2017.03.012
  • Primary Citation of Related Structures:  
    5WUU

  • PubMed Abstract: 

    As an epigenetic reader, BRD4 regulates the transcription of important downstream genes that are essential for the survival of tumor cells. Small molecular inhibitors targeting the first bromodomain of BRD4 (BRD4-BD1) have showed promising potentials in the therapies of BRD4-related cancers. Through AlphaScreen-based high-throughput screening assay, a novel small molecular inhibitor was identified, and named DCBD-005, which inhibited the binding between BRD4-BD1 and acetylated lysines with an IC 50 value of 0.81±0.03μM. The compound DCBD-005 effectively inhibited the viability, caused cell cycle arrest, and induced apoptosis in human leukemia MV4-11 cells. Moreover, the crystal structure of compound DCBD-005 with the BRD4-BD1 was determined at 1.72Å resolution, which revealed the binding mechanism of the leading compound, and also provided solid basis for further structure-based optimization. These results indicated that this novel BRD4-BD1 inhibitor DCBD-005 is promising to be developed into a drug candidate in the treatment of BRD4-related diseases.


  • Organizational Affiliation

    School of Pharmacy, Nanchang University, 461 Bayi Road, Nanchang 330006, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7UU
Query on 7UU

Download Ideal Coordinates CCD File 
B [auth A]~{N}-methyl-~{N}-[3-[(2-oxidanylidenechromen-4-yl)amino]propyl]thiophene-2-carboxamide
C18 H18 N2 O3 S
GHTHAUJPTBYQOJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
7UU BindingDB:  5WUU IC50: 810 (nM) from 1 assay(s)
Binding MOAD:  5WUU IC50: 810 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.981α = 90
b = 47.422β = 90
c = 78.836γ = 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: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-06-14
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description