5A81

Crystal structure of human ATAD2 bromodomain in complex with 8-(3R,4R) -3-(cyclohexylmethoxy)piperidin-4-yl-amino-3-methyl-1,2-dihydro-1,7- naphthyridin-2-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

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This is version 1.2 of the entry. See complete history


Literature

Structure-Based Optimization of Naphthyridones Into Potent Atad2 Bromodomain Inhibitors.

Bamborough, P.Chung, C.Furze, R.C.Grandi, P.Michon, A.Sheppard, R.J.Barnett, H.Diallo, H.Dixon, D.P.Douault, C.Jones, E.J.Karamshi, B.Mitchell, D.J.Prinjha, R.K.Rau, C.Watson, R.J.Werner, T.Demont, E.H.

(2015) J Med Chem 58: 6151

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b00773
  • Primary Citation of Related Structures:  
    5A81, 5A82, 5A83, 5A85

  • PubMed Abstract: 

    ATAD2 is a bromodomain-containing protein whose overexpression is linked to poor outcomes in a number of different cancer types. To date, no potent and selective inhibitors of the bromodomain have been reported. This article describes the structure-based optimization of a series of naphthyridones from micromolar leads with no selectivity over the BET bromodomains to inhibitors with sub-100 nM ATAD2 potency and 100-fold BET selectivity.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2130Homo sapiensMutation(s): 0 
EC: 3.6.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PL18 (Homo sapiens)
Explore Q6PL18 
Go to UniProtKB:  Q6PL18
PHAROS:  Q6PL18
GTEx:  ENSG00000156802 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PL18
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
78J BindingDB:  5A81 Kd: min: 2900, max: 3162 (nM) from 3 assay(s)
IC50: min: 2512, max: 3981 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.54α = 90
b = 79.54β = 90
c = 138.22γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-08-26
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other