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 
  • R-Value Observed: 0.271 

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:  
    5AD3, 5AD2

  • 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 EC 50 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, Waltham, Massachusetts, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BROMODOMAIN-CONTAINING PROTEIN 4AB127Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
NIH Common Fund Data Resources
PHAROS  O60885
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K6K
Query on K6K

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:  7.900000095367432   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.271 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.64α = 90
b = 41.826β = 90
c = 59.591γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

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