EED in complex with a triazolopyrimidine

Experimental Data Snapshot

  • Resolution: 1.52 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report

This is version 2.0 of the entry. See complete history


Rapid Identification of Novel Allosteric PRC2 Inhibitors.

Read, J.A.Tart, J.Rawlins, P.B.Gregson, C.Jones, K.Gao, N.Zhu, X.Tomlinson, R.Code, E.Cheung, T.Chen, H.Kawatkar, S.P.Bloecher, A.Bagal, S.O'Donovan, D.H.Robinson, J.

(2019) ACS Chem Biol 14: 2134-2140

  • DOI: https://doi.org/10.1021/acschembio.9b00468
  • Primary Citation of Related Structures:  
    6SFB, 6SFC

  • PubMed Abstract: 

    Enhancer of zeste homologue 2 (EZH2), the catalytic subunit of polycomb repressive complex 2 (PRC2), regulates chromatin state and gene expression by methylating histone H3 lysine 27. EZH2 is overexpressed or mutated in various hematological malignancies and solid cancers. Our previous efforts to identify inhibitors of PRC2 methyltransferase activity by high-throughput screening (HTS) resulted in large numbers of false positives and thus a significant hit deconvolution challenge. More recently, others have reported compounds that bind to another PRC2 core subunit, EED, and allosterically inhibit EZH2 activity. This mechanism is particularly appealing as it appears to retain potency in cell lines that have acquired resistance to orthosteric EZH2 inhibition. By designing a fluorescence polarization probe based on the reported EED binding compounds, we were able to quickly and cleanly re-triage our previously challenging HTS hit list and identify novel allosteric PRC2 inhibitors.

  • Organizational Affiliation

    Discovery Biology, Discovery Sciences , R&D, AstraZeneca , Cambridge , CB4 0WG U.K.

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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75530
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L9W (Subject of Investigation/LOI)
Query on L9W

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
C21 H19 N5 O3 S
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.52 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.308α = 90
b = 89.786β = 90
c = 98.84γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2019-09-25 
  • Deposition Author(s): Read, J.A.

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references
  • Version 2.0: 2021-07-14
    Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary