5TTW

Crystal Structure of EED in Complex with UNC4859


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of Peptidomimetic Ligands of EED as Allosteric Inhibitors of PRC2.

Barnash, K.D.The, J.Norris-Drouin, J.L.Cholensky, S.H.Worley, B.M.Li, F.Stuckey, J.I.Brown, P.J.Vedadi, M.Arrowsmith, C.H.Frye, S.V.James, L.I.

(2017) ACS Comb Sci 19: 161-172

  • DOI: 10.1021/acscombsci.6b00174

  • PubMed Abstract: 
  • The function of EED within polycomb repressive complex 2 (PRC2) is mediated by a complex network of protein-protein interactions. Allosteric activation of PRC2 by binding of methylated proteins to the embryonic ectoderm development (EED) aromatic cag ...

    The function of EED within polycomb repressive complex 2 (PRC2) is mediated by a complex network of protein-protein interactions. Allosteric activation of PRC2 by binding of methylated proteins to the embryonic ectoderm development (EED) aromatic cage is essential for full catalytic activity, but details of this regulation are not fully understood. EED's recognition of the product of PRC2 activity, histone H3 lysine 27 trimethylation (H3K27me3), stimulates PRC2 methyltransferase activity at adjacent nucleosomes leading to H3K27me3 propagation and, ultimately, gene repression. By coupling combinatorial chemistry and structure-based design, we optimized a low-affinity methylated jumonji, AT-rich interactive domain 2 (Jarid2) peptide to a smaller, more potent peptidomimetic ligand (Kd = 1.14 ± 0.14 μM) of the aromatic cage of EED. Our strategy illustrates the effectiveness of applying combinatorial chemistry to achieve both ligand potency and property optimization. Furthermore, the resulting ligands, UNC5114 and UNC5115, demonstrate that targeted disruption of EED's reader function can lead to allosteric inhibition of PRC2 catalytic activity.


    Organizational Affiliation

    Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polycomb protein EED
A, C
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
UNC4859
B, D
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
UNX
Query on UNX

Download SDF File 
Download CCD File 
A, C, D
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
B, D
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
NLW
Query on NLW
B, D
L-peptide linkingC6 H14 N2 OLeu
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 176.486α = 90.00
b = 56.212β = 105.33
c = 76.687γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
MOLREPphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-02-22
    Type: Database references
  • Version 1.2: 2017-03-29
    Type: Database references