5K0M

Targeting the PRC2 complex through a novel protein-protein interaction inhibitor of EED


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.133 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The EED protein-protein interaction inhibitor A-395 inactivates the PRC2 complex.

He, Y.Selvaraju, S.Curtin, M.L.Jakob, C.G.Zhu, H.Comess, K.M.Shaw, B.The, J.Lima-Fernandes, E.Szewczyk, M.M.Cheng, D.Klinge, K.L.Li, H.Q.Pliushchev, M.Algire, M.A.Maag, D.Guo, J.Dietrich, J.Panchal, S.C.Petros, A.M.Sweis, R.F.Torrent, M.Bigelow, L.J.Senisterra, G.Li, F.Kennedy, S.Wu, Q.Osterling, D.J.Lindley, D.J.Gao, W.Galasinski, S.Barsyte-Lovejoy, D.Vedadi, M.Buchanan, F.G.Arrowsmith, C.H.Chiang, G.G.Sun, C.Pappano, W.N.

(2017) Nat. Chem. Biol. 13: 389-395

  • DOI: 10.1038/nchembio.2306

  • PubMed Abstract: 
  • Polycomb repressive complex 2 (PRC2) is a regulator of epigenetic states required for development and homeostasis. PRC2 trimethylates histone H3 at lysine 27 (H3K27me3), which leads to gene silencing, and is dysregulated in many cancers. The embryoni ...

    Polycomb repressive complex 2 (PRC2) is a regulator of epigenetic states required for development and homeostasis. PRC2 trimethylates histone H3 at lysine 27 (H3K27me3), which leads to gene silencing, and is dysregulated in many cancers. The embryonic ectoderm development (EED) protein is an essential subunit of PRC2 that has both a scaffolding function and an H3K27me3-binding function. Here we report the identification of A-395, a potent antagonist of the H3K27me3 binding functions of EED. Structural studies demonstrate that A-395 binds to EED in the H3K27me3-binding pocket, thereby preventing allosteric activation of the catalytic activity of PRC2. Phenotypic effects observed in vitro and in vivo are similar to those of known PRC2 enzymatic inhibitors; however, A-395 retains potent activity against cell lines resistant to the catalytic inhibitors. A-395 represents a first-in-class antagonist of PRC2 protein-protein interactions (PPI) for use as a chemical probe to investigate the roles of EED-containing protein complexes.


    Organizational Affiliation

    eFFECTOR Therapeutics, San Diego, California, USA.,Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,AbbVie Inc., North Chicago, Illinois, USA.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polycomb protein EED
A
372Homo sapiensMutation(s): 0 
Gene Names: EED
Find proteins for O75530 (Homo sapiens)
Go to Gene View: EED
Go to UniProtKB:  O75530
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6PU
Query on 6PU

Download SDF File 
Download CCD File 
A
(3R,4S)-1-[(1S)-7-fluoro-2,3-dihydro-1H-inden-1-yl]-N,N-dimethyl-4-{4-[4-(methylsulfonyl)piperazin-1-yl]phenyl}pyrrolidin-3-amine
C26 H35 F N4 O2 S
REVJNSVNICWODC-VJTSUQJLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.133 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.843α = 90.00
b = 84.911β = 90.00
c = 91.627γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2018-05-16
    Type: Data collection, Database references