7NR4

X-RAY STRUCTURE OF PRMT6 IN COMPLEX WITH indazole type inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Rational Design and Synthesis of Selective PRMT4 Inhibitors: A New Chemotype for Development of Cancer Therapeutics*.

Sutherland, M.Li, A.Kaghad, A.Panagopoulos, D.Li, F.Szewczyk, M.Smil, D.Scholten, C.Bouche, L.Stellfeld, T.Arrowsmith, C.H.Barsyte, D.Vedadi, M.Hartung, I.V.Steuber, H.Britton, R.Santhakumar, V.

(2021) ChemMedChem 

  • DOI: 10.1002/cmdc.202100018
  • Primary Citation of Related Structures:  
    7NR4

  • PubMed Abstract: 
  • Protein arginine N-methyl transferase 4 (PRMT4) asymmetrically dimethylates the arginine residues of histone H3 and nonhistone proteins. The overexpression of PRMT4 in several cancers has stimulated interest in the discovery of inhibitors as biological tools and, potentially, therapeutics ...

    Protein arginine N-methyl transferase 4 (PRMT4) asymmetrically dimethylates the arginine residues of histone H3 and nonhistone proteins. The overexpression of PRMT4 in several cancers has stimulated interest in the discovery of inhibitors as biological tools and, potentially, therapeutics. Although several PRMT4 inhibitors have been reported, most display poor selectivity against other members of the PRMT family of methyl transferases. Herein, we report the structure-based design of a new class of alanine-containing 3-arylindoles as potent and selective PRMT4 inhibitors, and describe key structure-activity relationships for this class of compounds.


    Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, Suite 700, 101 College Street, Toronto, ON M5G 1L7, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein arginine N-methyltransferase 6 ABCD376Homo sapiensMutation(s): 0 
Gene Names: PRMT6HRMT1L6
EC: 2.1.1 (PDB Primary Data), 2.1.1.125 (PDB Primary Data), 2.1.1.319 (UniProt)
Find proteins for Q96LA8 (Homo sapiens)
Explore Q96LA8 
Go to UniProtKB:  Q96LA8
NIH Common Fund Data Resources
PHAROS:  Q96LA8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UO2
Query on UO2

Download Ideal Coordinates CCD File 
A, B, C, D
(2~{S})-2-azanyl-~{N}-[3-[3-(dimethylsulfamoyl)phenyl]-2~{H}-indazol-5-yl]propanamide
C18 H21 N5 O3 S
HKVYLIVZRUYPKC-NSHDSACASA-N
 Ligand Interaction
SAH
Query on SAH

Download Ideal Coordinates CCD File 
A, B, C, D
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.936α = 90
b = 135.252β = 98.28
c = 83.197γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2021-03-02 
  • Released Date: 2021-04-07 
  • Deposition Author(s): Steuber, H.

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release