4X63

Crystal structure of PRMT5:MEP50 with EPZ015666 and SAH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

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
  • Structures With Same Primary Citation

  • 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 c ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein arginine N-methyltransferase 5A645Homo 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
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Methylosome protein 50B350Homo 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
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
3XV
Query on 3XV

Download 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3XVIC50:  100   nM  BindingDB
SAHIC50:  50000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.403α = 90
b = 138.065β = 90
c = 178.252γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data 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 

  • 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