5IJ8

Structure of the primary oncogenic mutant Y641N Hs/AcPRC2 in complex with a pyridone inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Polycomb repressive complex 2 structure with inhibitor reveals a mechanism of activation and drug resistance.

Brooun, A.Gajiwala, K.S.Deng, Y.L.Liu, W.Bolanos, B.Bingham, P.He, Y.A.Diehl, W.Grable, N.Kung, P.P.Sutton, S.Maegley, K.A.Yu, X.Stewart, A.E.

(2016) Nat Commun 7: 11384-11384

  • DOI: 10.1038/ncomms11384
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Polycomb repressive complex 2 (PRC2) mediates gene silencing through chromatin reorganization by methylation of histone H3 lysine 27 (H3K27). Overexpression of the complex and point mutations in the individual subunits of PRC2 have been shown to cont ...

    Polycomb repressive complex 2 (PRC2) mediates gene silencing through chromatin reorganization by methylation of histone H3 lysine 27 (H3K27). Overexpression of the complex and point mutations in the individual subunits of PRC2 have been shown to contribute to tumorigenesis. Several inhibitors of the PRC2 activity have shown efficacy in EZH2-mutated lymphomas and are currently in clinical development, although the molecular basis of inhibitor recognition remains unknown. Here we report the crystal structures of the inhibitor-bound wild-type and Y641N PRC2. The structures illuminate an important role played by a stretch of 17 residues in the N-terminal region of EZH2, we call the activation loop, in the stimulation of the enzyme activity, inhibitor recognition and the potential development of the mutation-mediated drug resistance. The work presented here provides new avenues for the design and development of next-generation PRC2 inhibitors through establishment of a structure-based drug design platform.


    Organizational Affiliation

    Worldwide Medicinal Chemistry, Worldwide Research and Development, Pfizer Inc., San Diego, California 92121, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Enhancer of Zeste Homolog 2 (EZH2),Histone-lysine N-methyltransferase EZH2
A, B
643Anolis carolinensisMutation(s): 1 
Gene Names: EZH2
Find proteins for G1KPH4 (Anolis carolinensis)
Go to Gene View: EZH2
Go to UniProtKB:  G1KPH4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polycomb protein EED
E, F
362Homo sapiensMutation(s): 0 
Gene Names: EED
Find proteins for O75530 (Homo sapiens)
Go to Gene View: EED
Go to UniProtKB:  O75530
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Polycomb protein SUZ12
S, T
191Homo sapiensMutation(s): 1 
Gene Names: SUZ12 (CHET9, JJAZ1, KIAA0160)
Find proteins for Q15022 (Homo sapiens)
Go to Gene View: SUZ12
Go to UniProtKB:  Q15022
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
6BN
Query on 6BN

Download SDF File 
Download CCD File 
A, B
5,8-dichloro-2-[(4-ethyl-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-({1-[(2R)-2-hydroxypropanoyl]piperidin-4-yl}oxy)-3,4-dihydroisoquinolin-1(2H)-one
C26 H31 Cl2 N3 O5
KBXFBLWYHFRQAH-OAHLLOKOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 71.331α = 90.00
b = 115.133β = 103.35
c = 153.939γ = 90.00
Software Package:
Software NamePurpose
AutoPROCdata scaling
BUSTERrefinement
Aimlessdata scaling
CNXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-05-11
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Derived calculations, Refinement description