5MLJ

Bromodomain of Human GCN5 with 4-bromo-2-methyl-5-(((3R,5R)-1-methyl-5-phenylpiperidin-3-yl)amino)pyridazin-3(2H)-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of a Potent, Cell Penetrant, and Selective p300/CBP-Associated Factor (PCAF)/General Control Nonderepressible 5 (GCN5) Bromodomain Chemical Probe.

Humphreys, P.G.Bamborough, P.Chung, C.W.Craggs, P.D.Gordon, L.Grandi, P.Hayhow, T.G.Hussain, J.Jones, K.L.Lindon, M.Michon, A.M.Renaux, J.F.Suckling, C.J.Tough, D.F.Prinjha, R.K.

(2017) J. Med. Chem. 60: 695-709

  • DOI: 10.1021/acs.jmedchem.6b01566
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • p300/CREB binding protein associated factor (PCAF/KAT2B) and general control nonderepressible 5 (GCN5/KAT2A) are multidomain proteins that have been implicated in retroviral infection, inflammation pathways, and cancer development. However, outside o ...

    p300/CREB binding protein associated factor (PCAF/KAT2B) and general control nonderepressible 5 (GCN5/KAT2A) are multidomain proteins that have been implicated in retroviral infection, inflammation pathways, and cancer development. However, outside of viral replication, little is known about the dependence of these effects on the C-terminal bromodomain. Herein, we report GSK4027 as a chemical probe for the PCAF/GCN5 bromodomain, together with GSK4028 as an enantiomeric negative control. The probe was optimized from a weakly potent, nonselective pyridazinone hit to deliver high potency for the PCAF/GCN5 bromodomain, high solubility, cellular target engagement, and ≥18000-fold selectivity over the BET family, together with ≥70-fold selectivity over the wider bromodomain families.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone acetyltransferase KAT2A
A, B
112Homo sapiensMutation(s): 0 
Gene Names: KAT2A (GCN5, GCN5L2)
EC: 2.3.1.48
Find proteins for Q92830 (Homo sapiens)
Go to Gene View: KAT2A
Go to UniProtKB:  Q92830
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9ST
Query on 9ST

Download SDF File 
Download CCD File 
A, B
4-bromo-2-methyl-5-[[(3~{R},5~{R})-1-methyl-5-phenyl-piperidin-3-yl]amino]pyridazin-3-one
C17 H21 Br N4 O
VZAFGXCWAWRULT-UONOGXRCSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.630α = 90.00
b = 74.000β = 90.00
c = 76.310γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-12-06 
  • Released Date: 2017-12-20 
  • Deposition Author(s): Chung, C.-W.

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Database references