5A5S

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 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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: 10.1021/acs.jmedchem.5b00772
  • Primary Citation of 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 ...

    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

    ∥Drug Metabolism and Pharmacokinetics (DMPK), GlaxoSmithKline, Park Road, Ware, Hertfordshire SG12 0DP, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BROMODOMAIN-CONTAINING PROTEIN 4A127Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NP8 (Subject of Investigation/LOI)
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
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
NP8 BindingDB:  5A5S IC50: min: 1259, max: 1.58e+4 (nM) from 2 assay(s)
Binding MOAD:  5A5S IC50: 1300 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 
  • 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