5H17

EED in complex with PRC2 allosteric inhibitor EED210


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Discovery and Molecular Basis of a Diverse Set of Polycomb Repressive Complex 2 Inhibitors Recognition by EED

Li, L.Zhang, H.Zhang, M.Zhao, M.Feng, L.Luo, X.Gao, Z.Huang, Y.Ardayfio, O.Zhang, J.H.Lin, Y.Fan, H.Mi, Y.Li, G.Liu, L.Feng, L.Luo, F.Teng, L.Qi, W.Ottl, J.Lingel, A.Bussiere, D.E.Yu, Z.Atadja, P.Lu, C.Li, E.Gu, J.Zhao, K.

(2017) PLoS ONE 12: e0169855-e0169855

  • DOI: 10.1371/journal.pone.0169855
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Polycomb repressive complex 2 (PRC2), a histone H3 lysine 27 methyltransferase, plays a key role in gene regulation and is a known epigenetics drug target for cancer therapy. The WD40 domain-containing protein EED is the regulatory subunit of PRC2. I ...

    Polycomb repressive complex 2 (PRC2), a histone H3 lysine 27 methyltransferase, plays a key role in gene regulation and is a known epigenetics drug target for cancer therapy. The WD40 domain-containing protein EED is the regulatory subunit of PRC2. It binds to the tri-methylated lysine 27 of the histone H3 (H3K27me3), and through which stimulates the activity of PRC2 allosterically. Recently, we disclosed a novel PRC2 inhibitor EED226 which binds to the K27me3-pocket on EED and showed strong antitumor activity in xenograft mice model. Here, we further report the identification and validation of four other EED binders along with EED162, the parental compound of EED226. The crystal structures for all these five compounds in complex with EED revealed a common deep pocket induced by the binding of this diverse set of compounds. This pocket was created after significant conformational rearrangement of the aromatic cage residues (Y365, Y148 and F97) in the H3K27me3 binding pocket of EED, the width of which was delineated by the side chains of these rearranged residues. In addition, all five compounds interact with the Arg367 at the bottom of the pocket. Each compound also displays unique features in its interaction with EED, suggesting the dynamics of the H3K27me3 pocket in accommodating the binding of different compounds. Our results provide structural insights for rational design of novel EED binder for the inhibition of PRC2 complex activity.


    Organizational Affiliation

    Novartis Institutes for BioMedical Research, Basel, Switzerland.,Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America.,Novartis Institutes for BioMedical Research, Emeryville, California, United States of America.,China Novartis Institutes for BioMedical Research, Shanghai, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polycomb protein EED
A
367Homo sapiensMutation(s): 0 
Gene Names: EED
Find proteins for O75530 (Homo sapiens)
Go to Gene View: EED
Go to UniProtKB:  O75530
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase EZH2
B
29Homo sapiensMutation(s): 0 
Gene Names: EZH2 (KMT6)
EC: 2.1.1.43
Find proteins for Q15910 (Homo sapiens)
Go to Gene View: EZH2
Go to UniProtKB:  Q15910
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LQE
Query on LQE

Download SDF File 
Download CCD File 
A
(3R,4aS,10aS)-6-methoxy-3-[(3-methoxyphenyl)methyl]-1-methyl-3,4,4a,5,10,10a-hexahydro-2H-benzo[g]quinoline
C23 H29 N O2
QZUPQRHYHMMHGC-JLMWRMLUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LQEIC50: 890 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.189 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 50.560α = 90.00
b = 92.280β = 90.00
c = 180.480γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
MOLREPphasing
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-25
    Type: Initial release