4X60

Crystal structure of PRMT5:MEP50 with EPZ015666 and sinefungin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A selective inhibitor of PRMT5 with in vivo and in vitro potency in MCL models.

Chan-Penebre, E.Kuplast, K.G.Majer, C.R.Boriack-Sjodin, P.A.Wigle, T.J.Johnston, L.D.Rioux, N.Munchhof, M.J.Jin, L.Jacques, S.L.West, K.A.Lingaraj, T.Stickland, K.Ribich, S.A.Raimondi, A.Scott, M.P.Waters, N.J.Pollock, R.M.Smith, J.J.Barbash, O.Pappalardi, M.Ho, T.F.Nurse, K.Oza, K.P.Gallagher, K.T.Kruger, R.Moyer, M.P.Copeland, R.A.Chesworth, R.Duncan, K.W.

(2015) Nat Chem Biol 11: 432-437

  • DOI: 10.1038/nchembio.1810
  • Primary Citation of Related Structures:  
    4X60, 4X61, 4X63

  • PubMed Abstract: 
  • Protein arginine methyltransferase-5 (PRMT5) is reported to have a role in diverse cellular processes, including tumorigenesis, and its overexpression is observed in cell lines and primary patient samples derived from lymphomas, particularly mantle cell lymphoma (MCL) ...

    Protein arginine methyltransferase-5 (PRMT5) is reported to have a role in diverse cellular processes, including tumorigenesis, and its overexpression is observed in cell lines and primary patient samples derived from lymphomas, particularly mantle cell lymphoma (MCL). Here we describe the identification and characterization of a potent and selective inhibitor of PRMT5 with antiproliferative effects in both in vitro and in vivo models of MCL. EPZ015666 (GSK3235025) is an orally available inhibitor of PRMT5 enzymatic activity in biochemical assays with a half-maximal inhibitory concentration (IC50) of 22 nM and broad selectivity against a panel of other histone methyltransferases. Treatment of MCL cell lines with EPZ015666 led to inhibition of SmD3 methylation and cell death, with IC50 values in the nanomolar range. Oral dosing with EPZ015666 demonstrated dose-dependent antitumor activity in multiple MCL xenograft models. EPZ015666 represents a validated chemical probe for further study of PRMT5 biology and arginine methylation in cancer and other diseases.


    Organizational Affiliation

    Departments of Biology and Molecular Discovery, Epizyme, Inc., Cambridge, Massachusetts, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein arginine N-methyltransferase 5 A645Homo sapiensMutation(s): 0 
Gene Names: PRMT5HRMT1L5IBP72JBP1SKB1
EC: 2.1.1 (PDB Primary Data), 2.1.1.125 (PDB Primary Data), 2.1.1.320 (UniProt)
Find proteins for O14744 (Homo sapiens)
Explore O14744 
Go to UniProtKB:  O14744
NIH Common Fund Data Resources
PHAROS:  O14744
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Methylosome protein 50 B350Homo sapiensMutation(s): 0 
Gene Names: WDR77MEP50WD45HKMT1069Nbla10071
Find proteins for Q9BQA1 (Homo sapiens)
Explore Q9BQA1 
Go to UniProtKB:  Q9BQA1
NIH Common Fund Data Resources
PHAROS:  Q9BQA1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3XV
Query on 3XV

Download Ideal Coordinates CCD File 
A
N-[(2S)-3-(3,4-dihydroisoquinolin-2(1H)-yl)-2-hydroxypropyl]-6-(oxetan-3-ylamino)pyrimidine-4-carboxamide
C20 H25 N5 O3
ZKXZLIFRWWKZRY-KRWDZBQOSA-N
 Ligand Interaction
SFG
Query on SFG

Download Ideal Coordinates CCD File 
A
SINEFUNGIN
C15 H23 N7 O5
LMXOHSDXUQEUSF-YECHIGJVSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3XVKd:  1   nM  Binding MOAD
3XVIC50:  100   nM  BindingDB
3XVIC50:  22   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.67α = 90
b = 137.96β = 90
c = 179.01γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2014-12-06 
  • Released Date: 2015-04-22 
  • Deposition Author(s): Boriack-Sjodin, P.A.

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-22
    Type: Initial release
  • Version 1.1: 2015-05-13
    Changes: Database references
  • Version 1.2: 2015-05-27
    Changes: Structure summary