5LJ0

Crystal structure of human ATAD2 bromodomain in complex with 8-(((3R,4R,5S)-3-((4,4-difluorocyclohexyl)methoxy)-5-methoxypiperidin-4-yl)amino)-3-methyl-5-(5-methylpyridin-3-yl)-1,7-naphthyridin-2(1H)-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

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Ligand Structure Quality Assessment 


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, 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 ...

    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
ATPase family AAA domain-containing protein 2A130Homo sapiensMutation(s): 0 
Gene Names: ATAD2L16PRO2000
EC: 3.6.1.3 (PDB Primary Data), 3.6.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PL18 (Homo sapiens)
Explore Q6PL18 
Go to UniProtKB:  Q6PL18
PHAROS:  Q6PL18
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6XX (Subject of Investigation/LOI)
Query on 6XX

Download Ideal Coordinates CCD File 
F [auth A]8-(((3R,4R,5S)-3-((4,4-difluorocyclohexyl)methoxy)-5-methoxypiperidin-4-yl)amino)-3-methyl-5-(5-methylpyridin-3-yl)-1,7-naphthyridin-2(1H)-one
C28 H35 F2 N5 O3
YDPMMWAOCCOULO-JBRSBNLGSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A], E [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
6XX BindingDB:  5LJ0 IC50: 50 (nM) from 1 assay(s)
Binding MOAD:  5LJ0 IC50: 10 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.158α = 90
b = 79.158β = 90
c = 135.857γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2016-07-17 
  • Released Date: 2016-08-31 
  • Deposition Author(s): Chung, C.

Revision History  (Full details and data files)

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