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


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 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • DOI: 10.1002/anie.201603928
  • Primary Citation of Related Structures:  
    5LJ0, 5LJ2, 5LJ1

  • 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 ...

    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.


    Organizational Affiliation

    GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain-containing protein 4A127Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6XW
Query on 6XW

Download CCD File 
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
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6XWIC50:  16000   nM  Binding MOAD
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 = 37.52α = 90
b = 44.28β = 90
c = 78.1γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2016-09-14
    Changes: Database references