7P2R

Crystal structure of mouse PRMT6 in complex with inhibitor EML980

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

wwPDB Validation 

Currently 7P2R does not have a validation slider image.


This is version 1.0 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 

  • DOI: 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 ...

    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: 

    Université de Strasbourg, 67400 Illkirch, France.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein arginine N-methyltransferase 6A, B348Mus musculusMutation(s): 2 
Gene Names: Prmt6, Hrmt1l6
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4R7 (Subject of Investigation/LOI)
Query on 4R7
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		methyl 6-[4-[[N-[2-[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]ethyl]carbamimidoyl]amino]butylcarbamoylamino]-4-oxidanyl-naphthalene-2-carboxylate
C29 H36 N10 O7
QVOKJKWHZRTVQQ-HUBRGWSESA-N		 Ligand Interaction
SAH
Query on SAH
Download Ideal Coordinates CCD File 
D [auth B]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.797α = 90
b = 118.687β = 102.79
c = 72.052γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
StructureStudiodata collection
DIALSdata reduction
DIALSdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-10-INSB-005
Agence Nationale de la Recherche (ANR)FranceANR-10-LABX-0030-INRT
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: 2022-05-11
    Type: Initial release