Polycomb protein EED in complex with inhibitor: 2-[4-(4-{(3S,4R)-4-(dimethylamino)-1-[(2-fluoro-6-methylphenyl)methyl]pyrrolidin-3-yl}phenyl)-1H-pyrazol-1-yl]acetamide

Experimental Data Snapshot

  • Resolution: 1.64 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


SAR of amino pyrrolidines as potent and novel protein-protein interaction inhibitors of the PRC2 complex through EED binding.

Curtin, M.L.Pliushchev, M.A.Li, H.Q.Torrent, M.Dietrich, J.D.Jakob, C.G.Zhu, H.Zhao, H.Wang, Y.Ji, Z.Clark, R.F.Sarris, K.A.Selvaraju, S.Shaw, B.Algire, M.A.He, Y.Richardson, P.L.Sweis, R.F.Sun, C.Chiang, G.G.Michaelides, M.R.

(2017) Bioorg Med Chem Lett 27: 1576-1583

  • DOI: https://doi.org/10.1016/j.bmcl.2017.02.030
  • Primary Citation of Related Structures:  
    5U69, 5U6D, 5U8A, 5U8F

  • PubMed Abstract: 

    Herein we disclose SAR studies of a series of dimethylamino pyrrolidines which we recently reported as novel inhibitors of the PRC2 complex through disruption of EED/H3K27me3 binding. Modification of the indole and benzyl moieties of screening hit 1 provided analogs with substantially improved binding and cellular activities. This work culminated in the identification of compound 2, our nanomolar proof-of-concept (PoC) inhibitor which provided on-target tumor growth inhibition in a mouse xenograft model. X-ray crystal structures of several inhibitors bound in the EED active-site are also discussed.

  • Organizational Affiliation

    AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL 60064, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb protein EED369Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 7XG

Download Ideal Coordinates CCD File 
B [auth A]2-[4-(4-{(3S,4R)-4-(dimethylamino)-1-[(2-fluoro-6-methylphenyl)methyl]pyrrolidin-3-yl}phenyl)-1H-pyrazol-1-yl]acetamide
C25 H30 F N5 O
Binding Affinity Annotations 
IDSourceBinding Affinity
7XG BindingDB:  5U6D Ki: 2.6 (nM) from 1 assay(s)
Binding MOAD:  5U6D Ki: 2.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.64 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.663α = 90
b = 85.161β = 90
c = 91.711γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-03-22
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description