5AD3

Bivalent binding to BET bromodomains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.269 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Potent and Selective Bivalent Inhibitors of Bet Bromodomains

Waring, M.J.Chen, H.Rabow, A.A.Walker, G.Bobby, R.Boiko, S.Bradbury, R.H.Callis, R.Clark, E.Dale, I.Daniels, D.L.Dulak, A.Flavell, L.Holdgate, G.Jowitt, T.A.Kikhney, A.Mcalister, M.Ogg, D.Patel, J.Petteruti, P.Robb, G.R.Robers, M.B.Saif, S.Stratton, N.Svergun, D.I.Wang, W.Whittaker, D.Wilson, D.M.Yao, Y.

(2016) Nat.Chem.Biol. 12: 1097

  • DOI: 10.1038/nchembio.2210
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Proteins of the bromodomain and extraterminal (BET) family, in particular bromodomain-containing protein 4 (BRD4), are of great interest as biological targets. BET proteins contain two separate bromodomains, and existing inhibitors bind to them monov ...

    Proteins of the bromodomain and extraterminal (BET) family, in particular bromodomain-containing protein 4 (BRD4), are of great interest as biological targets. BET proteins contain two separate bromodomains, and existing inhibitors bind to them monovalently. Here we describe the discovery and characterization of probe compound biBET, capable of engaging both bromodomains simultaneously in a bivalent, in cis binding mode. The evidence provided here was obtained in a variety of biophysical and cellular experiments. The bivalent binding results in very high cellular potency for BRD4 binding and pharmacological responses such as disruption of BRD4-mediator complex subunit 1 foci with an EC50 of 100 pM. These compounds will be of considerable utility as BET/BRD4 chemical probes. This work illustrates a novel concept in ligand design-simultaneous targeting of two separate domains with a drug-like small molecule-providing precedent for a potentially more effective paradigm for developing ligands for other multi-domain proteins.


    Organizational Affiliation

    AstraZeneca, Alderley Park, UK.




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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K6K
Query on K6K

Download SDF File 
Download CCD File 
B
3-methoxy-N-[2-[4-[1-(3-methoxy-[1,2,4]triazolo[4,3-b]pyridazin-6-yl)-4-piperidyl]phenoxy]ethyl]-N-methyl-[1,2,4]triazolo[4,3-b]pyridazin-6-amine
C26 H30 N10 O3
LQHDIGAYVSAVRJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
K6KKd: 7.9 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.269 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 109.640α = 90.00
b = 41.826β = 90.00
c = 59.591γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
BUSTERrefinement
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2016-10-26
    Type: Database references
  • Version 1.2: 2016-11-09
    Type: Database references
  • Version 1.3: 2016-11-30
    Type: Database references