5H25

EED in complex with PRC2 allosteric inhibitor compound 11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of First-in-Class, Potent, and Orally Bioavailable Embryonic Ectoderm Development (EED) Inhibitor with Robust Anticancer Efficacy

Huang, Y.Zhang, J.Yu, Z.Zhang, H.Wang, Y.Lingel, A.Qi, W.Gu, J.Zhao, K.Shultz, M.D.Wang, L.Fu, X.Sun, Y.Zhang, Q.Jiang, X.Zhang, J.Zhang, C.Li, L.Zeng, J.Feng, L.Zhang, C.Liu, Y.Zhang, M.Zhang, L.Zhao, M.Gao, Z.Liu, X.Fang, D.Guo, H.Mi, Y.Gabriel, T.Dillon, M.P.Atadja, P.Oyang, C.

(2017) J. Med. Chem. 60: 2215-2226

  • DOI: 10.1021/acs.jmedchem.6b01576
  • Primary Citation of Related Structures:  
  • Also Cited By: 5H19

  • PubMed Abstract: 
  • Overexpression and somatic heterozygous mutations of EZH2, the catalytic subunit of polycomb repressive complex 2 (PRC2), are associated with several tumor types. EZH2 inhibitor, EPZ-6438 (tazemetostat), demonstrated clinical efficacy in patients wit ...

    Overexpression and somatic heterozygous mutations of EZH2, the catalytic subunit of polycomb repressive complex 2 (PRC2), are associated with several tumor types. EZH2 inhibitor, EPZ-6438 (tazemetostat), demonstrated clinical efficacy in patients with acceptable safety profile as monotherapy. EED, another subunit of PRC2 complex, is essential for its histone methyltransferase activity through direct binding to trimethylated lysine 27 on histone 3 (H3K27Me3). Herein we disclose the discovery of a first-in-class potent, selective, and orally bioavailable EED inhibitor compound 43 (EED226). Guided by X-ray crystallography, compound 43 was discovered by fragmentation and regrowth of compound 7, a PRC2 HTS hit that directly binds EED. The ensuing scaffold hopping followed by multiparameter optimization led to the discovery of 43. Compound 43 induces robust and sustained tumor regression in EZH2 MUT preclinical DLBCL model. For the first time we demonstrate that specific and direct inhibition of EED can be effective as an anticancer strategy.


    Organizational Affiliation

    Novartis Institutes for BioMedical Research , 5300 Chiron Way, Emeryville, California 94608, United States.,Novartis Institutes for BioMedical Research , 4218 Jinke Road, Shanghai 201203, 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
LQH
Query on LQH

Download SDF File 
Download CCD File 
A, B
5-(2-fluorophenyl)-2,3-dihydroimidazo[2,1-a]isoquinoline
C17 H13 F N2
CRASKXTVWBAFRS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 94.747α = 90.00
b = 179.379β = 90.00
c = 50.396γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
BUSTERrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

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: 2017-04-05
    Type: Database references