5ML0

Bromodomain of Mouse PCAF with (R)-4-chloro-2-methyl-5-((1-methylpiperidin-3-yl)amino)pyridazin-3(2H)-one

• PDB DOI: https://doi.org/10.2210/pdb5ML0/pdb

• Classification: TRANSCRIPTION
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-12-05 Released: 2017-12-20 
• Deposition Author(s): Chung, C.-W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.222 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

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

• PubMed: 28002667 
• DOI: https://doi.org/10.1021/acs.jmedchem.6b01566
• Primary Citation of 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 13.57 kDa 
• Atom Count: 1,175 
• Modelled Residue Count: 108 
• Deposited Residue Count: 110 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone acetyltransferase KAT2B	A	110	Mus musculus	Mutation(s): 0  Gene Names: Kat2b, Pcaf EC: 2.3.1.48 (PDB Primary Data), 2.3.1.57 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9JHD1 (Mus musculus) Explore Q9JHD1  Go to UniProtKB:  Q9JHD1
IMPC:  MGI:1343094

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P2L	B [auth A]	4-chlorol-2-methyl-5-[[(3~{R})-1-methylpiperidin-3-yl]amino]pyridazin-3-one C11 H17 Cl N4 O LEPPHANDICKARV-MRVPVSSYSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.222 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.481	α = 90
b = 93.481	β = 90
c = 32.783	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references