7NUD

Crystal structure of mouse PRMT6 in complex with inhibitor EML734


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Turning Nonselective Inhibitors of Type I Protein Arginine Methyltransferases into Potent and Selective Inhibitors of Protein Arginine Methyltransferase 4 through a Deconstruction-Reconstruction and Fragment-Growing Approach.

Iannelli, G.Milite, C.Marechal, N.Cura, V.Bonnefond, L.Troffer-Charlier, N.Feoli, A.Rescigno, D.Wang, Y.Cipriano, A.Viviano, M.Bedford, M.T.Cavarelli, J.Castellano, S.Sbardella, G.

(2022) J Med Chem 65: 11574-11606

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00252
  • Primary Citation of Related Structures:  
    7NUD, 7NUE, 7P2R, 7PPQ, 7PPY, 7PU8, 7PUC, 7PUQ, 7PV6

  • PubMed Abstract: 

    Protein arginine methyltransferases (PRMTs) are important therapeutic targets, playing a crucial role in the regulation of many cellular processes and being linked to many diseases. Yet, there is still much to be understood regarding their functions and the biological pathways in which they are involved, as well as on the structural requirements that could drive the development of selective modulators of PRMT activity. Here we report a deconstruction-reconstruction approach that, starting from a series of type I PRMT inhibitors previously identified by us, allowed for the identification of potent and selective inhibitors of PRMT4, which regardless of the low cell permeability show an evident reduction of arginine methylation levels in MCF7 cells and a marked reduction of proliferation. We also report crystal structures with various PRMTs supporting the observed specificity and selectivity.


  • Organizational Affiliation

    Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein arginine N-methyltransferase 6
A, B
386Mus musculusMutation(s): 1 
Gene Names: Prmt6Hrmt1l6
EC: 2.1.1.319
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NZB1 (Mus musculus)
Explore Q6NZB1 
Go to UniProtKB:  Q6NZB1
IMPC:  MGI:2139971
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NZB1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LRZ (Subject of Investigation/LOI)
Query on LRZ

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
methyl 6-[3-[[~{N}-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl]carbamimidoyl]amino]propylcarbamoylamino]-4-oxidanyl-naphthalene-2-carboxylate
C27 H32 N10 O7
GJPQENHVEQGHGP-UMCMBGNQSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.766α = 90
b = 118.147β = 104.32
c = 71.998γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-10-LABX-0030-INRT
Agence Nationale de la Recherche (ANR)FranceANR-10-INSB-005
Agence Nationale de la Recherche (ANR)FranceANR-19-CE11-0010-01 JC
Fondation ARCFrancePJA 20161204817

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-23
    Type: Initial release
  • Version 1.1: 2022-05-11
    Changes: Database references
  • Version 1.2: 2022-09-21
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description