4O77

Crystal structure of the first bromodomain of human BRD4 in complex with SB 202190


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.153 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Acetyl-lysine Binding Site of Bromodomain-Containing Protein 4 (BRD4) Interacts with Diverse Kinase Inhibitors.

Ember, S.W.Zhu, J.Y.Olesen, S.H.Martin, M.P.Becker, A.Berndt, N.Georg, G.I.Schonbrunn, E.

(2014) ACS Chem Biol 9: 1160-1171

  • DOI: https://doi.org/10.1021/cb500072z
  • Primary Citation of Related Structures:  
    4O70, 4O71, 4O72, 4O74, 4O75, 4O76, 4O77, 4O78, 4O7A, 4O7B, 4O7C, 4O7E, 4O7F, 4PS5

  • PubMed Abstract: 

    Members of the bromodomain and extra terminal (BET) family of proteins are essential for the recognition of acetylated lysine (KAc) residues in histones and have emerged as promising drug targets in cancer, inflammation, and contraception research. In co-crystallization screening campaigns using the first bromodomain of BRD4 (BRD4-1) against kinase inhibitor libraries, we identified and characterized 14 kinase inhibitors (10 distinct chemical scaffolds) as ligands of the KAc binding site. Among these, the PLK1 inhibitor BI2536 and the JAK2 inhibitor TG101209 displayed strongest inhibitory potential against BRD4 (IC50=25 nM and 130 nM, respectively) and high selectivity for BET bromodomains. Comparative structural analysis revealed markedly different binding modes of kinase hinge-binding scaffolds in the KAc binding site, suggesting that BET proteins are potential off-targets of diverse kinase inhibitors. Combined, these findings provide a new structural framework for the rational design of next-generation BET-selective and dual-activity BET-kinase inhibitors.


  • Organizational Affiliation

    Drug Discovery Department and §Chemical Biology Core, H. Lee Moffitt Cancer Center and Research Institute , Tampa, Florida 33612, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4
A, B
127Homo 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
2RE
Query on 2RE

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
4-[4-(4-fluorophenyl)-5-(pyridin-4-yl)-1H-imidazol-2-yl]phenol
C20 H14 F N3 O
QHKYPYXTTXKZST-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
2RE BindingDB:  4O77 Kd: 3400 (nM) from 1 assay(s)
IC50: min: 2500, max: 3400 (nM) from 2 assay(s)
Binding MOAD:  4O77 IC50: 2500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.153 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.45α = 90
b = 59.51β = 90
c = 108.38γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-03-19
    Changes: Database references
  • Version 1.2: 2014-05-28
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description