4HSG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

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Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    4HSG

  • 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 in cancer via interaction with the DAL-1 tumor suppressor protein ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PRMT3 proteinA340Homo sapiensMutation(s): 0 
Gene Names: PRMT3HRMT1L3
EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for O60678 (Homo sapiens)
Explore O60678 
Go to UniProtKB:  O60678
PHAROS:  O60678
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60678
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KTD
Query on KTD

Download Ideal Coordinates CCD File 
B [auth A]1-(1,2,3-benzothiadiazol-6-yl)-3-(2-oxo-2-phenylethyl)urea
C15 H12 N4 O2 S
PKHSKYFMULMNOC-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A]
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
KTD BindingDB:  4HSG IC50: 480 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.699α = 90
b = 70.699β = 90
c = 172.946γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Revision History  (Full details and data files)

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