5FE2

Crystal structure of human PCAF bromodomain in complex with fragment BR013 (fragment 3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-Based Identification of Inhibitory Fragments Targeting the p300/CBP-Associated Factor Bromodomain.

Chaikuad, A.Lang, S.Brennan, P.E.Temperini, C.Fedorov, O.Hollander, J.Nachane, R.Abell, C.Muller, S.Siegal, G.Knapp, S.

(2016) J.Med.Chem. 59: 1648-1653

  • DOI: 10.1021/acs.jmedchem.5b01719
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The P300/CBP-associated factor plays a central role in retroviral infection and cancer development, and the C-terminal bromodomain provides an opportunity for selective targeting. Here, we report several new classes of acetyl-lysine mimetic ligands r ...

    The P300/CBP-associated factor plays a central role in retroviral infection and cancer development, and the C-terminal bromodomain provides an opportunity for selective targeting. Here, we report several new classes of acetyl-lysine mimetic ligands ranging from mM to low micromolar affinity that were identified using fragment screening approaches. The binding modes of the most attractive fragments were determined using high resolution crystal structures providing chemical starting points and structural models for the development of potent and selective PCAF inhibitors.


    Organizational Affiliation

    Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University and Buchmann Institute for Molecular Life Sciences , Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany.,Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K.,Leiden Institute of Chemistry, Leiden University , Einsteinweg 55, 2333 CC Leiden, Netherlands.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium and Target Discovery Institute, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, U.K.,ZoBio , Einsteinweg 55, 2333 CC Leiden, Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone acetyltransferase KAT2B
A, B
119Homo sapiensMutation(s): 0 
Gene Names: KAT2B (PCAF)
EC: 2.3.1.48
Find proteins for Q92831 (Homo sapiens)
Go to Gene View: KAT2B
Go to UniProtKB:  Q92831
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
5WV
Query on 5WV

Download SDF File 
Download CCD File 
A, B
2-methyl-3~{H}-isoindol-1-one
C9 H9 N O
JHMBTUMIVBSJFS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.207 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 99.450α = 90.00
b = 99.450β = 90.00
c = 100.510γ = 120.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
PHASERphasing
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-03-30
    Type: Database references