5LS6

Structure of Human Polycomb Repressive Complex 2 (PRC2) with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.47 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Identification of (R)-N-((4-Methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-2-methyl-1-(1-(1-(2,2,2-trifluoroethyl)piperidin-4-yl)ethyl)-1H-indole-3-carboxamide (CPI-1205), a Potent and Selective Inhibitor of Histone Methyltransferase EZH2, Suitable for Phase I Clinical Trials for B-Cell Lymphomas.

Vaswani, R.G.Gehling, V.S.Dakin, L.A.Cook, A.S.Nasveschuk, C.G.Duplessis, M.Iyer, P.Balasubramanian, S.Zhao, F.Good, A.C.Campbell, R.Lee, C.Cantone, N.Cummings, R.T.Normant, E.Bellon, S.F.Albrecht, B.K.Harmange, J.C.Trojer, P.Audia, J.E.Zhang, Y.Justin, N.Chen, S.Wilson, J.R.Gamblin, S.J.

(2016) J. Med. Chem. 59: 9928-9941

  • DOI: 10.1021/acs.jmedchem.6b01315

  • PubMed Abstract: 
  • Polycomb repressive complex 2 (PRC2) has been shown to play a major role in transcriptional silencing in part by installing methylation marks on lysine 27 of histone 3. Dysregulation of PRC2 function correlates with certain malignancies and poor prog ...

    Polycomb repressive complex 2 (PRC2) has been shown to play a major role in transcriptional silencing in part by installing methylation marks on lysine 27 of histone 3. Dysregulation of PRC2 function correlates with certain malignancies and poor prognosis. EZH2 is the catalytic engine of the PRC2 complex and thus represents a key candidate oncology target for pharmacological intervention. Here we report the optimization of our indole-based EZH2 inhibitor series that led to the identification of CPI-1205, a highly potent (biochemical IC50 = 0.002 μM, cellular EC50 = 0.032 μM) and selective inhibitor of EZH2. This compound demonstrates robust antitumor effects in a Karpas-422 xenograft model when dosed at 160 mg/kg BID and is currently in Phase I clinical trials. Additionally, we disclose the co-crystal structure of our inhibitor series bound to the human PRC2 complex.


    Organizational Affiliation

    Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2
A, D, G, J
695Homo sapiensMutation(s): 0 
Gene Names: EZH2 (KMT6)
EC: 2.1.1.43
Find proteins for Q15910 (Homo sapiens)
Go to Gene View: EZH2
Go to UniProtKB:  Q15910
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polycomb protein EED
B, E, H, K
367Homo 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
C, F, I, L
129Homo sapiensMutation(s): 0 
Gene Names: SUZ12 (CHET9, JJAZ1, KIAA0160)
Find proteins for Q15022 (Homo sapiens)
Go to Gene View: SUZ12
Go to UniProtKB:  Q15022
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Jarid2 K116me3
Q, R, S, T
11Homo sapiensMutation(s): 0 
Gene Names: JARID2 (JMJ)
Find proteins for Q92833 (Homo sapiens)
Go to Gene View: JARID2
Go to UniProtKB:  Q92833
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, D, G, J
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
74D
Query on 74D

Download SDF File 
Download CCD File 
A, D, G, J
1-[(1~{R})-1-[1-[2,2-bis(fluoranyl)propyl]piperidin-4-yl]ethyl]-~{N}-[(4-methoxy-6-methyl-2-oxidanylidene-3~{H}-pyridin-3-yl)methyl]-2-methyl-indole-3-carboxamide
C28 H36 F2 N4 O3
MNZANYNOXFULDI-GCJKJVERSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
Q, R, S, T
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.47 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 131.310α = 90.00
b = 170.270β = 90.00
c = 275.540γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Advisory, Data collection, Derived calculations