7P3J

EED in complex with compound 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Diverse, Potent, and Efficacious Inhibitors That Target the EED Subunit of the Polycomb Repressive Complex 2 Methyltransferase.

Bagal, S.K.Gregson, C.O' Donovan, D.H.Pike, K.G.Bloecher, A.Barton, P.Borodovsky, A.Code, E.Fillery, S.M.Hsu, J.H.Kawatkar, S.P.Li, C.Longmire, D.Nai, Y.Nash, S.C.Pike, A.Robinson, J.Read, J.A.Rawlins, P.B.Shen, M.Tang, J.Wang, P.Woods, H.Williamson, B.

(2021) J Med Chem 64: 17146-17183

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01161
  • Primary Citation of Related Structures:  
    7P3C, 7P3G, 7P3J

  • PubMed Abstract: 

    Aberrant activity of the histone methyltransferase polycomb repressive complex 2 (PRC2) has been linked to several cancers, with small-molecule inhibitors of the catalytic subunit of the PRC2 enhancer of zeste homologue 2 (EZH2) being recently approved for the treatment of epithelioid sarcoma (ES) and follicular lymphoma (FL). Compounds binding to the EED subunit of PRC2 have recently emerged as allosteric inhibitors of PRC2 methyltransferase activity. In contrast to orthosteric inhibitors that target EZH2, small molecules that bind to EED retain their efficacy in EZH2 inhibitor-resistant cell lines. In this paper we disclose the discovery of potent and orally bioavailable EED ligands with good solubilities. The solubility of the EED ligands was optimized through a variety of design tactics, with the resulting compounds exhibiting in vivo efficacy in EZH2-driven tumors.


  • Organizational Affiliation

    AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0AA, United Kingdom.


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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
54N (Subject of Investigation/LOI)
Query on 54N

Download Ideal Coordinates CCD File 
G [auth B]8-[6-[(dimethylamino)methyl]-2-methyl-pyridin-3-yl]-5-[(5-fluoranyl-2,3-dihydro-1-benzofuran-4-yl)methylamino]-2H-pyrido[3,4-d]pyridazin-1-one
C25 H25 F N6 O2
TZPONVRYLBDEBM-UHFFFAOYSA-N
L9W
Query on L9W

Download Ideal Coordinates CCD File 
F [auth A]N-(2,3-dihydro-1-benzofuran-4-ylmethyl)-8-(4-methylsulfonylphenyl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine
C21 H19 N5 O3 S
GDDMEOORUYUIJL-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.1α = 90
b = 86.6β = 90
c = 97.29γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2021-12-08 
  • Deposition Author(s): Read, J.A.

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-08
    Type: Initial release
  • Version 1.1: 2021-12-22
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description