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 
  • R-Value Observed: 0.191 

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1038/ncomms11384
  • Primary Citation of Related Structures:  
    5IJ7, 5IJ8

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Enhancer of Zeste Homolog 2 (EZH2),Histone-lysine N-methyltransferase EZH2
A, B
643Anolis carolinensisHomo sapiens
This entity is chimeric
Mutation(s): 1 
Gene Names: EZH2KMT6
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.356 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q15910 (Homo sapiens)
Explore Q15910 
Go to UniProtKB:  Q15910
PHAROS:  Q15910
GTEx:  ENSG00000106462 
Find proteins for G1KPH4 (Anolis carolinensis)
Explore G1KPH4 
Go to UniProtKB:  G1KPH4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ15910G1KPH4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb protein EEDC [auth E],
D [auth F]
362Homo 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 
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UniProt GroupO75530
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb protein SUZ12E [auth S],
F [auth T]
191Homo sapiensMutation(s): 1 
Gene Names: SUZ12CHET9JJAZ1KIAA0160
UniProt & NIH Common Fund Data Resources
Find proteins for Q15022 (Homo sapiens)
Explore Q15022 
Go to UniProtKB:  Q15022
PHAROS:  Q15022
GTEx:  ENSG00000178691 
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UniProt GroupQ15022
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6BN
Query on 6BN

Download Ideal Coordinates CCD File 
G [auth A],
O [auth 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
ZN
Query on ZN

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.331α = 90
b = 115.133β = 103.35
c = 153.939γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata scaling
Aimlessdata scaling
CNXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-05-11
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references, Derived calculations, Refinement description