5LJ2

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 5-(5-aminopyridin-3-yl)-8-(((3R,4R)-3-((1,1-dioxidotetrahydro-2H-thiopyran-4-yl)methoxy)piperidin-4-yl)amino)-3-methyl-1,7-naphthyridin-2(1H)-one

• PDB DOI: https://doi.org/10.2210/pdb5LJ2/pdb

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


• Deposited: 2016-07-17 Released: 2016-08-31 
• Deposition Author(s): Chung, C., Bamborough, P., Demont, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 0.208 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 

Literature

A Chemical Probe for the ATAD2 Bromodomain.

Bamborough, P., Chung, C.W., Demont, E.H., Furze, R.C., Bannister, A.J., Che, K.H., Diallo, H., Douault, C., Grandi, P., Kouzarides, T., Michon, A.M., Mitchell, D.J., Prinjha, R.K., Rau, C., Robson, S., Sheppard, R.J., Upton, R., Watson, R.J.

(2016) Angew Chem Int Ed Engl 55: 11382-11386

• PubMed: 27530368 
• DOI: https://doi.org/10.1002/anie.201603928
• Primary Citation of Related Structures:  
  5LJ0, 5LJ1, 5LJ2


• PubMed Abstract: 
  

  ATAD2 is a cancer-associated protein whose bromodomain has been described as among the least druggable of that target class. Starting from a potent lead, permeability and selectivity were improved through a dual approach: 1) using CF2 as a sulfone bio-isostere to exploit the unique properties of fluorine, and 2) using 1,3-interactions to control the conformation of a piperidine ring. This resulted in the first reported low-nanomolar, selective and cell permeable chemical probe for ATAD2.

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Organizational Affiliation: 

GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, UK. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.8 kDa 
• Atom Count: 1,401 
• Modelled Residue Count: 127 
• Deposited Residue Count: 127 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	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
6XW	E [auth A]	5-(5-aminopyridin-3-yl)-8-(((3R,4R)-3-((1,1-dioxidotetrahydro-2H-thiopyran-4-yl)methoxy)piperidin-4-yl)amino)-3-methyl-1,7-naphthyridin-2(1H)-one C25 H32 N6 O4 S BTPIXSXGFYUFSV-FGZHOGPDSA-N
EDO	B [auth A], C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 0.208 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.52	α = 90
b = 44.28	β = 90
c = 78.1	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-31 
Deposition Author(s): Chung, C., Bamborough, P., Demont, E.

Revision History  

• Version 1.0: 2016-08-31
  Type: Initial release
  
• Version 1.1: 2016-09-14
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references