4HSG

Crystal structure of human PRMT3 in complex with an allosteric inhibitor (PRMT3- KTD)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Exploiting an allosteric binding site of PRMT3 yields potent and selective inhibitors.

Liu, F.Li, F.Ma, A.Dobrovetsky, E.Dong, A.Gao, C.Korboukh, I.Liu, J.Smil, D.Brown, P.J.Frye, S.V.Arrowsmith, C.H.Schapira, M.Vedadi, M.Jin, J.

(2013) J. Med. Chem. 56: 2110-2124

  • DOI: 10.1021/jm3018332

  • PubMed Abstract: 
  • Protein arginine methyltransferases (PRMTs) play an important role in diverse biological processes. Among the nine known human PRMTs, PRMT3 has been implicated in ribosomal biosynthesis via asymmetric dimethylation of the 40S ribosomal protein S2 and ...

    Protein arginine methyltransferases (PRMTs) play an important role in diverse biological processes. Among the nine known human PRMTs, PRMT3 has been implicated in ribosomal biosynthesis via asymmetric dimethylation of the 40S ribosomal protein S2 and in cancer via interaction with the DAL-1 tumor suppressor protein. However, few selective inhibitors of PRMTs have been discovered. We recently disclosed the first selective PRMT3 inhibitor, which occupies a novel allosteric binding site and is noncompetitive with both the peptide substrate and cofactor. Here we report comprehensive structure-activity relationship studies of this series, which resulted in the discovery of multiple PRMT3 inhibitors with submicromolar potencies. An X-ray crystal structure of compound 14u in complex with PRMT3 confirmed that this inhibitor occupied the same allosteric binding site as our initial lead compound. These studies provide the first experimental evidence that potent and selective inhibitors can be created by exploiting the allosteric binding site of PRMT3.


    Organizational Affiliation

    Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PRMT3 protein
A
340Homo sapiensMutation(s): 0 
Gene Names: PRMT3 (HRMT1L3)
EC: 2.1.1.-
Find proteins for O60678 (Homo sapiens)
Go to Gene View: PRMT3
Go to UniProtKB:  O60678
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNX
Query on UNX

Download SDF File 
Download CCD File 
A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
KTD
Query on KTD

Download SDF File 
Download CCD File 
A
1-(1,2,3-benzothiadiazol-6-yl)-3-(2-oxo-2-phenylethyl)urea
C15 H12 N4 O2 S
PKHSKYFMULMNOC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KTDIC50: 480 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.192 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 70.699α = 90.00
b = 70.699β = 90.00
c = 172.946γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2012-12-05
    Type: Initial release
  • Version 1.1: 2018-05-16
    Type: Data collection, Database references