5KHM

The first BET bromodomain of BRD4 bound to compound 13 in a bivalent manner


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Optimization of a Series of Bivalent Triazolopyridazine Based Bromodomain and Extraterminal Inhibitors: The Discovery of (3R)-4-[2-[4-[1-(3-Methoxy-[1,2,4]triazolo[4,3-b]pyridazin-6-yl)-4-piperidyl]phenoxy]ethyl]-1,3-dimethyl-piperazin-2-one (AZD5153).

Bradbury, R.H.Callis, R.Carr, G.R.Chen, H.Clark, E.Feron, L.Glossop, S.Graham, M.A.Hattersley, M.Jones, C.Lamont, S.G.Ouvry, G.Patel, A.Patel, J.Rabow, A.A.Roberts, C.A.Stokes, S.Stratton, N.Walker, G.E.Ward, L.Whalley, D.Whittaker, D.Wrigley, G.Waring, M.J.

(2016) J.Med.Chem. 59: 7801-7817

  • DOI: 10.1021/acs.jmedchem.6b00070

  • PubMed Abstract: 
  • Here we report the discovery and optimization of a series of bivalent bromodomain and extraterminal inhibitors. Starting with the observation of BRD4 activity of compounds from a previous program, the compounds were optimized for BRD4 potency and phy ...

    Here we report the discovery and optimization of a series of bivalent bromodomain and extraterminal inhibitors. Starting with the observation of BRD4 activity of compounds from a previous program, the compounds were optimized for BRD4 potency and physical properties. The optimized compound from this campaign exhibited excellent pharmacokinetic profile and exhibited high potency in vitro and in vivo effecting c-Myc downregulation and tumor growth inhibition in xenograft studies. This compound was selected as the development candidate, AZD5153. The series showed enhanced potency as a result of bivalent binding and a clear correlation between BRD4 activity and cellular potency.


    Organizational Affiliation

    Northern Institute for Cancer Research, School of Chemistry, Newcastle University , Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.,AstraZeneca , Gatehouse Park, Waltham, Massachusetts 02451, United States.,AstraZeneca , Chemin du Moulin de Vrilly, 51100 Reims, France.,AstraZeneca, Mereside , Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K.




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
XNH
Query on XNH

Download SDF File 
Download CCD File 
A
(3~{R})-4-[2-[4-[1-(3-methoxy-[1,2,4]triazolo[4,3-b]pyridazin-6-yl)piperidin-4-yl]phenoxy]ethyl]-1,3-dimethyl-piperazin-2-one
C25 H33 N7 O3
RSMYFSPOTCDHHJ-GOSISDBHSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
XNHKi: 5.01 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 41.754α = 90.00
b = 59.769β = 90.00
c = 107.151γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
Aimlessdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-06-15 
  • Released Date: 2016-09-21 
  • Deposition Author(s): Patel, J.

Revision History 

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2017-08-09
    Type: Database references, Derived calculations