7QJG

EED in complex with PRC2 allosteric inhibitor compound 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery of the Clinical Candidate MAK683: An EED-Directed, Allosteric, and Selective PRC2 Inhibitor for the Treatment of Advanced Malignancies.

Huang, Y.Sendzik, M.Zhang, J.Gao, Z.Sun, Y.Wang, L.Gu, J.Zhao, K.Yu, Z.Zhang, L.Zhang, Q.Blanz, J.Chen, Z.Dubost, V.Fang, D.Feng, L.Fu, X.Kiffe, M.Li, L.Luo, F.Luo, X.Mi, Y.Mistry, P.Pearson, D.Piaia, A.Scheufler, C.Terranova, R.Weiss, A.Zeng, J.Zhang, H.Zhang, J.Zhao, M.Dillon, M.P.Jeay, S.Qi, W.Moggs, J.Pissot-Soldermann, C.Li, E.Atadja, P.Lingel, A.Oyang, C.

(2022) J Med Chem 65: 5317-5333

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c02148
  • Primary Citation of Related Structures:  
    7QJG, 7QJU, 7QK4

  • PubMed Abstract: 

    Polycomb Repressive Complex 2 (PRC2) plays an important role in transcriptional regulation during animal development and in cell differentiation, and alteration of PRC2 activity has been associated with cancer. On a molecular level, PRC2 catalyzes methylation of histone H3 lysine 27 (H3K27), resulting in mono-, di-, or trimethylated forms of H3K27, of which the trimethylated form H3K27me3 leads to transcriptional repression of polycomb target genes. Previously, we have shown that binding of the low-molecular-weight compound EED226 to the H3K27me3 binding pocket of the regulatory subunit EED can effectively inhibit PRC2 activity in cells and reduce tumor growth in mouse xenograft models. Here, we report the stepwise optimization of the tool compound EED226 toward the potent and selective EED inhibitor MAK683 (compound 22 ) and its subsequent preclinical characterization. Based on a balanced PK/PD profile, efficacy, and mitigated risk of forming reactive metabolites, MAK683 has been selected for clinical development.


  • Organizational Affiliation

    Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb protein EED
A, B
366Homo 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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase EZH2
C, D
29Homo sapiensMutation(s): 0 
EC: 2.1.1.356
UniProt & NIH Common Fund Data Resources
Find proteins for Q15910 (Homo sapiens)
Explore Q15910 
Go to UniProtKB:  Q15910
PHAROS:  Q15910
GTEx:  ENSG00000106462 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15910
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.46α = 90
b = 178.446β = 90
c = 50.497γ = 90
Software Package:
Software NamePurpose
autoPROCdata processing
autoPROCdata processing
STARANISOdata scaling
autoPROCdata processing
BUSTERrefinement
autoPROCdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-13
    Type: Initial release
  • Version 1.1: 2022-04-27
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary