4X61

Crystal structure of PRMT5:MEP50 with EPZ015666 and SAM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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 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)
UniProt & NIH Common Fund Data Resources
Find proteins for O14744 (Homo sapiens)
Explore O14744 
Go to UniProtKB:  O14744
PHAROS:  O14744
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Methylosome protein 50B350Homo sapiensMutation(s): 0 
Gene Names: WDR77MEP50WD45HKMT1069Nbla10071
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQA1 (Homo sapiens)
Explore Q9BQA1 
Go to UniProtKB:  Q9BQA1
PHAROS:  Q9BQA1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM (Subject of Investigation/LOI)
Query on SAM

Download Ideal Coordinates CCD File 
C [auth A]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
3XV (Subject of Investigation/LOI)
Query on 3XV

Download Ideal Coordinates CCD File 
D [auth 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
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
3XV BindingDB:  4X61 IC50: min: 22, max: 100 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.317α = 90
b = 138.167β = 90
c = 178.007γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



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