5LV5

Crystal structure of mouse PRMT6 in complex with inhibitor LH1458


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.802 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Hijacking DNA methyltransferase transition state analogues to produce chemical scaffolds for PRMT inhibitors.

Halby, L.Marechal, N.Pechalrieu, D.Cura, V.Franchini, D.M.Faux, C.Alby, F.Troffer-Charlier, N.Kudithipudi, S.Jeltsch, A.Aouadi, W.Decroly, E.Guillemot, J.C.Page, P.Ferroud, C.Bonnefond, L.Guianvarc'h, D.Cavarelli, J.Arimondo, P.B.

(2018) Philos. Trans. R. Soc. Lond., B, Biol. Sci. 373: --

  • DOI: 10.1098/rstb.2017.0072
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DNA, RNA and histone methylation is implicated in various human diseases such as cancer or viral infections, playing a major role in cell process regulation, especially in modulation of gene expression. Here we developed a convergent synthetic pathwa ...

    DNA, RNA and histone methylation is implicated in various human diseases such as cancer or viral infections, playing a major role in cell process regulation, especially in modulation of gene expression. Here we developed a convergent synthetic pathway starting from a protected bromomethylcytosine derivative to synthesize transition state analogues of the DNA methyltransferases. This approach led to seven 5-methylcytosine-adenosine compounds that were, surprisingly, inactive against hDNMT1, hDNMT3Acat, TRDMT1 and other RNA human and viral methyltransferases. Interestingly, compound 4 and its derivative 2 showed an inhibitory activity against PRMT4 in the micromolar range. Crystal structures showed that compound 4 binds to the PRMT4 active site, displacing strongly the S -adenosyl-l-methionine cofactor, occupying its binding site, and interacting with the arginine substrate site through the cytosine moiety that probes the space filled by a substrate peptide methylation intermediate. Furthermore, the binding of the compounds induces important structural switches. These findings open new routes for the conception of new potent PRMT4 inhibitors based on the 5-methylcytosine-adenosine scaffold.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.


    Organizational Affiliation

    Laboratoire de chimie moléculaire, CMGPCE, EA7341, Conservatoire National des Arts et Métiers, 2 rue Conté, 75003 Paris, France.,Sorbonne Universités, UPMC Université Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules (LBM), 4 place Jussieu, 75005 Paris, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Laboratoire Architecture Fonction des Macromolécules Biologiques (AFMB-UMR 7257), Aix-Marseille Université & CNRS, 163 avenue de Luminy, 13288 Marseille cedex 09, France.,Maison Française d'Oxford, CNRS, MEAE, 2-10 Norham Road, Oxford, UK.,CNRS FRE3600 ETaC, bât. IBCG, 31062 Toulouse, France paola.arimondo@etac.cnrs.fr.,Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Université Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 75005 Paris, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France cava@igbmc.fr.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Institute of Biochemistry, Faculty of Chemistry, University Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany.,CNRS FRE3600 ETaC, bât. IBCG, 31062 Toulouse, France.,Churchill College, CB3 0DS Cambridge, UK.,Laboratoire Pierre Fabre, 3 avenue H. Curien, 31100 Toulouse, France.,Institut National de la Santé et de la Recherche Médicale, U 1258, Illkirch, France.,Université de Strasbourg, Illkirch, France.,Epiremed SAS, 1 Rue des Pénitents Blancs, 31000 Toulouse, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein arginine N-methyltransferase 6
A
403Mus musculusMutation(s): 0 
Gene Names: Prmt6 (Hrmt1l6)
EC: 2.1.1.319
Find proteins for Q6NZB1 (Mus musculus)
Go to UniProtKB:  Q6NZB1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
78G
Query on 78G

Download SDF File 
Download CCD File 
A
2-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]ethyl-[[4-azanyl-1-(methoxymethyl)-2-oxidanylidene-pyrimidin-5-yl]methyl]-[(3~{S})-3-azanyl-4-oxidanyl-4-oxidanylidene-butyl]azanium
C22 H33 N10 O7
GZMYJIXALPWXCM-WUMBASEESA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.802 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.154 
  • Space Group: I 41
Unit Cell:
Length (Å)Angle (°)
a = 77.703α = 90.00
b = 77.703β = 90.00
c = 117.692γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2018-05-02
    Type: Data collection, Database references