5U8F

Polycomb protein EED in complex with inhibitor: (3R,4S)-1-[(1S)-7-fluoro-2,3-dihydro-1H-inden-1-yl]-N,N-dimethyl-4-(1-methyl-1H-indol-3-yl)pyrrolidin-3-amine

• PDB DOI: https://doi.org/10.2210/pdb5U8F/pdb

• Classification: PROTEIN BINDING/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-12-14 Released: 2017-03-15 
• Deposition Author(s): Jakob, C.G., Zhu, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 0.176 
• R-Value Work: 0.153 
• R-Value Observed: 0.154 

Starting Model: experimental

Literature

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

• PubMed: 28254486 
• 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.

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Organizational Affiliation: 

AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL 60064, United States. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.96 kDa 
• Atom Count: 3,203 
• Modelled Residue Count: 358 
• Deposited Residue Count: 369 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycomb protein EED	A	369	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
82G	B [auth A]	(3R,4S)-1-[(1S)-7-fluoro-2,3-dihydro-1H-inden-1-yl]-N,N-dimethyl-4-(1-methyl-1H-indol-3-yl)pyrrolidin-3-amine C24 H28 F N3 XAWMNFFOVCNWGF-OIBXWCBGSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
82G	BindingDB:  5U8F	Ki: min: 1, max: 11 (nM) from 2 assay(s)
		Kd: 10 (nM) from 1 assay(s)
		IC50: min: 290, max: 660 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 0.176 
• R-Value Work: 0.153 
• R-Value Observed: 0.154 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.645	α = 90
b = 85.108	β = 90
c = 91.514	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-15 
Deposition Author(s): Jakob, C.G., Zhu, H.

Revision History  

• 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
• Version 1.3: 2024-10-30
  Changes: Structure summary