6SFC | pdb_00006sfc

EED in complex with a methyl-thiazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.228 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6SFC

Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

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 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
    • Structure and Biophysics, Discovery Sciences , R&D, AstraZeneca , Cambridge , CB4 0WG U.K.

Macromolecule Content 

  • Total Structure Weight: 85.43 kDa 
  • Atom Count: 5,948 
  • Modeled Residue Count: 694 
  • Deposited Residue Count: 732 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.228 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86α = 90
b = 86.18β = 90
c = 97.18γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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 2.0: 2021-07-14
    Changes: Advisory, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-05-15
    Changes: Data collection, Database references