5LV5

Crystal structure of mouse PRMT6 in complex with inhibitor LH1458

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

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:  
    5TBH, 5TBJ, 5TBI, 5LV2, 5LV4, 5LV3, 5LV5

  • 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 pathway st ...

    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: 

    Churchill College, CB3 0DS Cambridge, UK.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein arginine N-methyltransferase 6 A403Mus musculusMutation(s): 0 
Gene Names: Prmt6, Hrmt1l6
EC: 2.1.1.319
Find proteins for Q6NZB1 (Mus musculus)
Explore Q6NZB1 
Go to UniProtKB:  Q6NZB1
NIH Common Fund Data Resources
IMPC:  MGI:2139971
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
78G
Query on 78G
Download Ideal Coordinates 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: 1.80 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.703α = 90
b = 77.703β = 90
c = 117.692γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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