5MKX

1.68A STRUCTURE PCAF BROMODOMAIN WITH 4-chloro-2-methyl-5-(methylamino)pyridazin-3(2H)-one

• PDB DOI: https://doi.org/10.2210/pdb5MKX/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• 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: 1.68 Å
• R-Value Free: 0.206 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 

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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.12 kDa 
• Atom Count: 2,240 
• Modelled Residue Count: 213 
• Deposited Residue Count: 238 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone acetyltransferase KAT2B	A, B	119	Homo sapiens	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 Q92831 (Homo sapiens) Explore Q92831  Go to UniProtKB:  Q92831
PHAROS:  Q92831 GTEx:  ENSG00000114166

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	E [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
82I	C [auth A], F [auth B]	4-chloranyl-2-methyl-5-(methylamino)pyridazin-3-one C6 H8 Cl N3 O ACZYSEPOODWZET-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BU1	G [auth B]	1,4-BUTANEDIOL C4 H10 O2 WERYXYBDKMZEQL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.206 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.264	α = 90
b = 99.264	β = 90
c = 100.378	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: 2022-07-13
  Changes: Database references, Structure summary
• Version 1.3: 2024-06-19
  Changes: Data collection