5AD3 | pdb_00005ad3

Bivalent binding to BET bromodomains

• PDB DOI: https://doi.org/10.2210/pdb5AD3/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-08-19 Released: 2016-09-28 
• Deposition Author(s): Waring, M.J., Chen, H., Rabow, A.A., Walker, G., Bobby, R., Boiko, S., Bradbury, R.H., Callis, R., Dale, I., Daniels, D., Flavell, L., Holdgate, G., Jowitt, T.A., Kikhney, A., McAlister, M., Ogg, D., Patel, J., Petteruti, P., Robb, G.R., Robers, M., Stratton, N., Svergun, D.I., Wang, W., Whittaker, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 
  0.308 (Depositor), 0.359 (DCC) 
• R-Value Work: 
  0.269 (Depositor), 0.298 (DCC) 
• R-Value Observed: 
  0.271 (Depositor) 

Starting Model: experimental

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

• PubMed: 27775716 
• DOI: https://doi.org/10.1038/nchembio.2210
• Primary Citation Related Structures: 
  5AD2, 5AD3


• 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 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.

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Organizational Affiliation: 
• AstraZeneca, Alderley Park, UK.
Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Newcastle upon Tyne, UK.
AstraZeneca, Waltham, Massachusetts, USA.
Promega Corporation, Madison, Wisconsin, USA.
Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK.
European Molecular Biology Laboratory, Hamburg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.73 kDa 
• Atom Count: 2,402 
• Modeled Residue Count: 253 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BROMODOMAIN-CONTAINING PROTEIN 4	A, B	127	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
PHAROS:  O60885 GTEx:  ENSG00000141867

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K6K	C [auth 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free:  0.308 (Depositor), 0.359 (DCC) 
• R-Value Work:  0.269 (Depositor), 0.298 (DCC) 
• R-Value Observed: 0.271 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.64	α = 90
b = 41.826	β = 90
c = 59.591	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-28 
Deposition Author(s): Waring, M.J., Chen, H., Rabow, A.A., Walker, G., Bobby, R., Boiko, S., Bradbury, R.H., Callis, R., Dale, I., Daniels, D., Flavell, L., Holdgate, G., Jowitt, T.A., Kikhney, A., McAlister, M., Ogg, D., Patel, J., Petteruti, P., Robb, G.R., Robers, M., Stratton, N., Svergun, D.I., Wang, W., Whittaker, D.

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
• Version 1.4: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description