N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH : 8-(((1R,2R,3R,5S)-2-(2-(4,4-difluorocyclohexyl)ethyl)-8-azabicyclo[3.2.1]octan-3-yl)amino)-3-methyl-5-(5-methylpyridin-3-yl)-1,7-naphthyridin-2(1H)-one

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


Aiming to Miss a Moving Target: Bromo and Extra Terminal Domain (BET) Selectivity in Constrained ATAD2 Inhibitors.

Bamborough, P.Chung, C.W.Furze, R.C.Grandi, P.Michon, A.M.Watson, R.J.Mitchell, D.J.Barnett, H.Prinjha, R.K.Rau, C.Sheppard, R.J.Werner, T.Demont, E.H.

(2018) J Med Chem 61: 8321-8336

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b00862
  • Primary Citation of Related Structures:  
    6HDN, 6HDO, 6HDQ

  • PubMed Abstract: 

    ATAD2 is a cancer-associated protein whose bromodomain has been described as among the least druggable of its class. In our recent disclosure of the first chemical probe against this bromodomain, GSK8814 (6), we described the use of a conformationally constrained methoxy piperidine to gain selectivity over the BET bromodomains. Here we describe an orthogonal conformational restriction strategy of the piperidine ring to give potent and selective tropane inhibitors and show structural insights into why this was more challenging than expected. Greater understanding of why different rational approaches succeeded or failed should help in the future design of selectivity in the bromodomain family.

  • Organizational Affiliation

    Molecular Discovery Research, Cellzome GmbH , GlaxoSmithKline , Meyerhofstrasse 1 , 69117 Heidelberg , Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4127Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
PHAROS:  O60885
GTEx:  ENSG00000141867 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FZE

Download Ideal Coordinates CCD File 
C [auth A]8-(((1R,2R,3R,5S)-2-(2-(4,4-difluorocyclohexyl)ethyl)-8-azabicyclo[3.2.1]octan-3-yl)amino)-3-methyl-5-(5-methylpyridin-3-yl)-1,7-naphthyridin-2(1H)-one
C30 H37 F2 N5 O
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A]1,2-ETHANEDIOL
C2 H6 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
FZE Binding MOAD:  6HDQ IC50: 5010 (nM) from 1 assay(s)
BindingDB:  6HDQ IC50: 5012 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.36α = 90
b = 112.7β = 90
c = 30.42γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2018-09-26 
  • Deposition Author(s): Chung, C.

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2018-10-10
    Changes: Data collection, Database references