6W7F

Structure of EED bound to inhibitor 5285


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

EEDi-5285: An Exceptionally Potent, Efficacious, and Orally Active Small-Molecule Inhibitor of Embryonic Ectoderm Development.

Rej, R.K.Wang, C.Lu, J.Wang, M.Petrunak, E.Zawacki, K.P.McEachern, D.Fernandez-Salas, E.Yang, C.Y.Wang, L.Li, R.Chinnaswamy, K.Wen, B.Sun, D.Stuckey, J.Zhou, Y.Chen, J.Tang, G.Wang, S.

(2020) J Med Chem 63: 7252-7267

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00479
  • Primary Citation of Related Structures:  
    6W7F, 6W7G

  • PubMed Abstract: 

    Inhibition of embryonic ectoderm development (EED) is a new cancer therapeutic strategy. Herein, we report our discovery of EEDi-5285 as an exceptionally potent, efficacious, and orally active EED inhibitor. EEDi-5285 binds to the EED protein with an IC 50 value of 0.2 nM and inhibits cell growth with IC 50 values of 20 pM and 0.5 nM in the Pfeiffer and KARPAS422 lymphoma cell lines, respectively, carrying an EZH2 mutation. EEDi-5285 is approximately 100 times more potent than EED226 in binding to EED and >300 times more potent than EED226 in inhibition of cell growth in the KARPAS422 cell line. EEDi-5285 has excellent pharmacokinetics and achieves complete and durable tumor regression in the KARPAS422 xenograft model in mice with oral administration. The cocrystal structure of EEDi-5285 in a complex with EED defines the precise structural basis for their high binding affinity. EEDi-5285 is the most potent and efficacious EED inhibitor reported to date.


  • Organizational Affiliation

    Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb protein EED368Homo 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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q3D (Subject of Investigation/LOI)
Query on Q3D

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
8-(6-cyclopropylpyridin-3-yl)-N-[(5-fluoro-2,3-dihydro-1-benzofuran-4-yl)methyl]-1-(methylsulfonyl)imidazo[1,5-c]pyrimidin-5-amine
C24 H22 F N5 O3 S
BMLWIABJRSYZDK-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
Q3D BindingDB:  6W7F IC50: 0.2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.694α = 90
b = 85.354β = 90
c = 92.199γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description