5EGS

Human PRMT6 with bound fragment-type inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of a Potent Class I Protein Arginine Methyltransferase Fragment Inhibitor.

Ferreira de Freitas, R.Eram, M.S.Szewczyk, M.M.Steuber, H.Smil, D.Wu, H.Li, F.Senisterra, G.Dong, A.Brown, P.J.Hitchcock, M.Moosmayer, D.Stegmann, C.M.Egner, U.Arrowsmith, C.Barsyte-Lovejoy, D.Vedadi, M.Schapira, M.

(2016) J.Med.Chem. 59: 1176-1183

  • DOI: 10.1021/acs.jmedchem.5b01772

  • PubMed Abstract: 
  • Protein methyltransferases (PMTs) are a promising target class in oncology and other disease areas. They are composed of SET domain methyltransferases and structurally unrelated Rossman-fold enzymes that include protein arginine methyltransferases (P ...

    Protein methyltransferases (PMTs) are a promising target class in oncology and other disease areas. They are composed of SET domain methyltransferases and structurally unrelated Rossman-fold enzymes that include protein arginine methyltransferases (PRMTs). In the absence of a well-defined medicinal chemistry tool-kit focused on PMTs, most current inhibitors were identified by screening large and diverse libraries of leadlike molecules. So far, no successful fragment-based approach was reported against this target class. Here, by deconstructing potent PRMT inhibitors, we find that chemical moieties occupying the substrate arginine-binding site can act as efficient fragment inhibitors. Screening a fragment library against PRMT6 produced numerous hits, including a 300 nM inhibitor (ligand efficiency of 0.56) that decreased global histone 3 arginine 2 methylation in cells, and can serve as a warhead for the development of PRMT chemical probes.


    Organizational Affiliation

    Department of Pharmacology and Toxicology, University of Toronto , Toronto, ON M5S 1A8, Canada.,Pharmaceuticals Division, Bayer Pharma AG, 13353 Berlin, Germany.,Structural Genomics Consortium, University of Toronto , Toronto, ON M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto , Toronto, ON M5G 1L7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein arginine N-methyltransferase 6
A, B, C, D
376Homo sapiensMutation(s): 0 
Gene Names: PRMT6 (HRMT1L6)
EC: 2.1.1.319
Find proteins for Q96LA8 (Homo sapiens)
Go to Gene View: PRMT6
Go to UniProtKB:  Q96LA8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5NR
Query on 5NR

Download SDF File 
Download CCD File 
A, B, C, D
2-[4-(phenylmethyl)piperidin-1-yl]ethanamine
C14 H22 N2
PCNDXYHWLSHXMV-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, B, C, D
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5NRIC50: 230 - 21000 nM (99) BINDINGDB
5NRKd: 970 nM (99) BINDINGDB
5NRIC50: 300 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 77.157α = 90.00
b = 135.616β = 98.91
c = 83.086γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-06-22
    Type: Database references