5GSA

EED in complex with an allosteric PRC2 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An allosteric PRC2 inhibitor targeting the H3K27me3 binding pocket of

Qi, W.Zhao, K.Gu, J.Huang, Y.Wang, Y.Zhang, H.Zhang, M.Zhang, J.Yu, Z.Li, L.Teng, L.Chuai, S.Zhang, C.Zhao, M.Chan, H.Chen, Z.Fang, D.Fei, Q.Feng, L.Feng, L.Gao, Y.Ge, H.Ge, X.Li, G.Lingel, A.Lin, Y.Liu, Y.Luo, F.Shi, M.Wang, L.Wang, Z.Yu, Y.Zeng, J.Zeng, C.Zhang, L.Zhang, Q.Zhou, S.Oyang, C.Atadja, P.Li, E.

(2017) Nat. Chem. Biol. 13: 381-388

  • DOI: 10.1038/nchembio.2304

  • PubMed Abstract: 
  • Polycomb repressive complex 2 (PRC2) consists of three core subunits, EZH2, EED and SUZ12, and plays pivotal roles in transcriptional regulation. The catalytic subunit EZH2 methylates histone H3 lysine 27 (H3K27), and its activity is further enhanced ...

    Polycomb repressive complex 2 (PRC2) consists of three core subunits, EZH2, EED and SUZ12, and plays pivotal roles in transcriptional regulation. The catalytic subunit EZH2 methylates histone H3 lysine 27 (H3K27), and its activity is further enhanced by the binding of EED to trimethylated H3K27 (H3K27me3). Small-molecule inhibitors that compete with the cofactor S-adenosylmethionine (SAM) have been reported. Here we report the discovery of EED226, a potent and selective PRC2 inhibitor that directly binds to the H3K27me3 binding pocket of EED. EED226 induces a conformational change upon binding EED, leading to loss of PRC2 activity. EED226 shows similar activity to SAM-competitive inhibitors in blocking H3K27 methylation of PRC2 target genes and inducing regression of human lymphoma xenograft tumors. Interestingly, EED226 also effectively inhibits PRC2 containing a mutant EZH2 protein resistant to SAM-competitive inhibitors. Together, we show that EED226 inhibits PRC2 activity via an allosteric mechanism and offers an opportunity for treatment of PRC2-dependent cancers.


    Organizational Affiliation

    Novartis Institutes for BioMedical Research, Shanghai, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polycomb protein EED
A, B
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
C, D
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
73K
Query on 73K

Download SDF File 
Download CCD File 
A, B
N-(furan-2-ylmethyl)-8-(4-methylsulfonylphenyl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine
C17 H15 N5 O3 S
DYIRSNMPIZZNBK-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
73KKd: 82.5 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 93.793α = 90.00
b = 177.908β = 90.00
c = 50.532γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALEPACKdata scaling
BUSTER-TNTrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2017-04-05
    Type: Database references