5MLJ | pdb_00005mlj

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: 1.80 Å
  • R-Value Free: 
    0.211 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/acs.jmedchem.6b01566
  • Primary Citation Related Structures: 
    5MKX, 5MKY, 5MKZ, 5ML0, 5MLI, 5MLJ

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 27.45 kDa 
  • Atom Count: 2,229 
  • Modeled Residue Count: 213 
  • Deposited Residue Count: 224 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone acetyltransferase KAT2A
A, B
112Homo sapiensMutation(s): 0 
Gene Names: KAT2A, GCN5, GCN5L2, HGCN5
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92830 (Homo sapiens)
Explore Q92830 
Go to UniProtKB:  Q92830
PHAROS:  Q92830
GTEx:  ENSG00000108773 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92830
Sequence Annotations
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Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
9ST BindingDB:  5MLJ Ki: min: 1.26, max: 1.3 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.211 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.63α = 90
b = 74β = 90
c = 76.31γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Advisory, Data collection, Database references