5KHM | pdb_00005khm

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

• PDB DOI: https://doi.org/10.2210/pdb5KHM/pdb

• Classification: Transcription Factor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.210 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.179 (Depositor) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

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

• PubMed: 27528113 
• DOI: https://doi.org/10.1021/acs.jmedchem.6b00070
• Primary Citation Related Structures: 
  5KHM


• 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 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 30.95 kDa 
• Atom Count: 2,494 
• Modeled Residue Count: 252 
• 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  Gene Names: BRD4, HUNK1
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XNH	C [auth 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
GOL	D [auth A], E [auth B], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
XNH	BindingDB:  5KHM	Ki: min: 5, max: 158 (nM) from 4 assay(s)
		IC50: min: 1.6, max: 1600 (nM) from 6 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.210 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.179 (Depositor) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.754	α = 90
b = 59.769	β = 90
c = 107.151	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: 2016-09-21 
Deposition Author(s): Patel, J.

Revision History  

• Version 1.0: 2016-09-21
  Type: Initial release
  
• Version 1.1: 2017-08-09
  Changes: Database references, Derived calculations
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description