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 
  • R-Value Observed: 0.136 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1038/nchembio.2306
  • Primary Citation of Related Structures:  
    5K0M

  • 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 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

    AbbVie Inc., North Chicago, Illinois, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb protein EED372Homo sapiensMutation(s): 0 
Gene Names: EED
UniProt & NIH Common Fund Data Resources
Find proteins for O75530 (Homo sapiens)
Explore O75530 
Go to UniProtKB:  O75530
PHAROS:  O75530
GTEx:  ENSG00000074266 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75530
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6PU
Query on 6PU

Download Ideal Coordinates CCD File 
B [auth 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.136 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.843α = 90
b = 84.911β = 90
c = 91.627γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description