5A5S | pdb_00005a5s

NN-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 5-5-methoxypyridin-3-yl-3- methyl-8-piperidin-4-ylamino-1,2-dihydro-1,7-naphthyridin-2-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 
    0.218 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5A5S

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Fragment-Based Discovery of Low-Micromolar Atad2 Bromodomain Inhibitors.

Demont, E.H.Chung, C.Furze, R.C.Grandi, P.Michon, A.Wellaway, C.Barrett, N.Bridges, A.M.Craggs, P.D.Diallo, H.Dixon, D.P.Douault, C.Emmons, A.J.Jones, E.J.Karamshi, B.V.Locke, K.Mitchell, D.J.Mouzon, B.H.Prinjha, R.K.Roberts, A.D.Sheppard, R.J.Watson, R.J.Bamborough, P.

(2015) J Med Chem 58: 5649

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b00772
  • Primary Citation Related Structures: 
    5A5N, 5A5O, 5A5P, 5A5Q, 5A5R, 5A5S

  • PubMed Abstract: 

    Overexpression of ATAD2 (ATPase family, AAA domain containing 2) has been linked to disease severity and progression in a wide range of cancers, and is implicated in the regulation of several drivers of cancer growth. Little is known of the dependence of these effects upon the ATAD2 bromodomain, which has been categorized as among the least tractable of its class. The absence of any potent, selective inhibitors limits clear understanding of the therapeutic potential of the bromodomain. Here, we describe the discovery of a hit from a fragment-based targeted array. Optimization of this produced the first known micromolar inhibitors of the ATAD2 bromodomain.


  • Organizational Affiliation
    • §Molecular Discovery Research, Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

Macromolecule Content 

  • Total Structure Weight: 15.53 kDa 
  • Atom Count: 1,250 
  • Modeled Residue Count: 127 
  • Deposited Residue Count: 127 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BROMODOMAIN-CONTAINING PROTEIN 4127Homo sapiensMutation(s): 0 
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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NP8

Query on NP8



Download:Ideal Coordinates CCD File
C [auth A]5-(5-methoxypyridin-3-yl)-3-methyl-8-[(piperidin-4-yl)amino]-1,2-dihydro-1,7-naphthyridin-2-one
C20 H23 N5 O2
FPQQERRFPULCIK-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
B [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free:  0.218 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.39α = 90
b = 49.39β = 90
c = 59.23γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-08-05
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other