6Q3Y

Crystal structure of the first bromodomain of human BRD4 in complex with the inhibitor 16i


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Designing Dual Inhibitors of Anaplastic Lymphoma Kinase (ALK) and Bromodomain-4 (BRD4) by Tuning Kinase Selectivity.

Watts, E.Heidenreich, D.Tucker, E.Raab, M.Strebhardt, K.Chesler, L.Knapp, S.Bellenie, B.Hoelder, S.

(2019) J.Med.Chem. 62: 2618-2637

  • DOI: 10.1021/acs.jmedchem.8b01947
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Concomitant inhibition of anaplastic lymphoma kinase (ALK) and bromodomain-4 (BRD4) is a potential therapeutic strategy for targeting two key oncogenic drivers that co-segregate in a significant fraction of high-risk neuroblastoma patients, mutation ...

    Concomitant inhibition of anaplastic lymphoma kinase (ALK) and bromodomain-4 (BRD4) is a potential therapeutic strategy for targeting two key oncogenic drivers that co-segregate in a significant fraction of high-risk neuroblastoma patients, mutation of ALK and amplification of MYCN. Starting from known dual polo-like kinase (PLK)-1-BRD4 inhibitor BI-2536, we employed structure-based design to redesign this series toward compounds with a dual ALK-BRD4 profile. These efforts led to compound ( R)-2-((2-ethoxy-4-(1-methylpiperidin-4-yl)phenyl)amino)-7-ethyl-5-methyl-8-((4-methylthiophen-2-yl)methyl)-7,8-dihydropteridin-6(5 H)-one (16k) demonstrating improved ALK activity and significantly reduced PLK-1 activity, while maintaining BRD4 activity and overall kinome selectivity. We demonstrate the compounds' on-target engagement with ALK and BRD4 in cells as well as favorable broad kinase and bromodomain selectivity.


    Organizational Affiliation

    Department of Gynecology and Obstetrics , Johann Wolfgang Goethe-University , Theodor-Stern Kai 7 , 60590 Frankfurt am Main , Germany.,Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research , London SM2 5NG , U.K.,Institute for Pharmaceutical Chemistry , Johann Wolfgang Goethe-University , Max-von-Laue-Strasse 9 , D-60438 Frankfurt am Main , Germany.,Paediatric and Solid Tumour Biology and Therapeutics Group , The Institute of Cancer Research , 15 Cotswold Road , London SM2 5NG , U.K.,Structural Genomics Consortium, BMLS , Goethe-University Frankfurt , 60438 Frankfurt , Germany.,German Cancer Network (DKTK) , Site Frankfurt/Mainz , D-60438 Frankfurt am Main , Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bromodomain-containing protein 4
A, B
127Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
HG5
Query on HG5

Download SDF File 
Download CCD File 
A, B
(7~{R})-2-[[2-ethoxy-4-(1-methylpiperidin-4-yl)phenyl]amino]-7-ethyl-5-methyl-8-(phenylmethyl)-7~{H}-pteridin-6-one
C30 H38 N6 O2
TWABWUVZWXSPTC-RUZDIDTESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.142 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 30.340α = 83.93
b = 39.530β = 75.64
c = 56.030γ = 89.75
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2019-03-27
    Type: Data collection, Database references