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 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/acs.jmedchem.6b01315
  • Primary Citation of Related Structures:  
    5LS6

  • 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 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 IC 50 = 0.002 μM, cellular EC 50 = 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
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: EZH2KMT6
EC: 2.1.1.43
UniProt & NIH Common Fund Data Resources
Find proteins for Q15910 (Homo sapiens)
Explore Q15910 
Go to UniProtKB:  Q15910
PHAROS:  Q15910
GTEx:  ENSG00000106462 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15910
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb protein EED
B, E, H, K
367Homo 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
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb protein SUZ12
C, F, I, L
129Homo sapiensMutation(s): 0 
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

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Jarid2 K116me3M [auth Q],
N [auth R],
O [auth S],
P [auth T]
11Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q92833 (Homo sapiens)
Explore Q92833 
Go to UniProtKB:  Q92833
PHAROS:  Q92833
GTEx:  ENSG00000008083 
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UniProt GroupQ92833
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
74D
Query on 74D

Download Ideal Coordinates CCD File 
HA [auth D],
QA [auth G],
Y [auth A],
ZA [auth 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
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
DA [auth D]
EA [auth D]
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
GA [auth D],
IA [auth G],
JA [auth G],
KA [auth G],
LA [auth G],
MA [auth G],
NA [auth G],
OA [auth G],
PA [auth G],
Q [auth A],
R [auth A],
RA [auth J],
S [auth A],
SA [auth J],
T [auth A],
TA [auth J],
U [auth A],
UA [auth J],
V [auth A],
VA [auth J],
W [auth A],
WA [auth J],
X [auth A],
XA [auth J],
YA [auth J],
Z [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
M3L
Query on M3L
M [auth Q],
N [auth R],
O [auth S],
P [auth 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 
  • R-Value Observed: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.31α = 90
b = 170.27β = 90
c = 275.54γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.2: 2019-07-10
    Changes: Data collection
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description