5U5T

Crystal structure of EED in complex with H3K27Me3 peptide and 3-(benzo[d][1,3]dioxol-4-ylmethyl)piperidine-1-carboximidamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure-Guided Design of EED Binders Allosterically Inhibiting the Epigenetic Polycomb Repressive Complex 2 (PRC2) Methyltransferase.

Lingel, A.Sendzik, M.Huang, Y.Shultz, M.D.Cantwell, J.Dillon, M.P.Fu, X.Fuller, J.Gabriel, T.Gu, J.Jiang, X.Li, L.Liang, F.McKenna, M.Qi, W.Rao, W.Sheng, X.Shu, W.Sutton, J.Taft, B.Wang, L.Zeng, J.Zhang, H.Zhang, M.Zhao, K.Lindvall, M.Bussiere, D.E.

(2017) J. Med. Chem. 60: 415-427

  • DOI: 10.1021/acs.jmedchem.6b01473
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • PRC2 is a multisubunit methyltransferase involved in epigenetic regulation of early embryonic development and cell growth. The catalytic subunit EZH2 methylates primarily lysine 27 of histone H3, leading to chromatin compaction and repression of tumo ...

    PRC2 is a multisubunit methyltransferase involved in epigenetic regulation of early embryonic development and cell growth. The catalytic subunit EZH2 methylates primarily lysine 27 of histone H3, leading to chromatin compaction and repression of tumor suppressor genes. Inhibiting this activity by small molecules targeting EZH2 was shown to result in antitumor efficacy. Here, we describe the optimization of a chemical series representing a new class of PRC2 inhibitors which acts allosterically via the trimethyllysine pocket of the noncatalytic EED subunit. Deconstruction of a larger and complex screening hit to a simple fragment-sized molecule followed by structure-guided regrowth and careful property modulation were employed to yield compounds which achieve submicromolar inhibition in functional assays and cellular activity. The resulting molecules can serve as a simplified entry point for lead optimization and can be utilized to study this new mechanism of PRC2 inhibition and the associated biology in detail.


    Organizational Affiliation

    Novartis Institutes for BioMedical Research , 2418 Jinke Road, Shanghai 201203, China.,Novartis Institutes for BioMedical Research , 5300 Chiron Way, Emeryville, California 94608, United States.




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
30Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YT3
Query on YT3

Download SDF File 
Download CCD File 
B
YTTRIUM (III) ION
Y
GRTBAGCGDOYUBE-UHFFFAOYSA-N
 Ligand Interaction
7W7
Query on 7W7

Download SDF File 
Download CCD File 
A, B
(3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide
C14 H19 N3 O2
LRVQENWFPVOJJS-SNVBAGLBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
7W7IC50: 3900 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.168 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 92.810α = 90.00
b = 177.909β = 90.00
c = 50.340γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
BUSTERrefinement
AMoREphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-12-07 
  • Released Date: 2017-01-11 
  • Deposition Author(s): Bussiere, D., Shu, W.

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-01-18
    Type: Database references
  • Version 1.2: 2017-01-25
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Data collection