8G2F

Crystal Structure of PRMT3 with Compound II710


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

Starting Model: experimental
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Literature

A unique binding pocket induced by a noncanonical SAH mimic to develop potent and selective PRMT inhibitors.

Deng, Y.Song, X.Iyamu, I.D.Dong, A.Min, J.Huang, R.

(2023) Acta Pharm Sin B 13: 4893-4905

  • DOI: https://doi.org/10.1016/j.apsb.2023.07.022
  • Primary Citation of Related Structures:  
    8G2F, 8G2G, 8G2H, 8G2I

  • PubMed Abstract: 

    Protein arginine methyltransferases (PRMTs) are attractive targets for developing therapeutic agents, but selective PRMT inhibitors targeting the cofactor SAM binding site are limited. Herein, we report the discovery of a noncanonical but less polar SAH surrogate YD1113 by replacing the benzyl guanidine of a pan-PRMT inhibitor with a benzyl urea, potently and selectively inhibiting PRMT3/4/5. Importantly, crystal structures reveal that the benzyl urea moiety of YD1113 induces a unique and novel hydrophobic binding pocket in PRMT3/4, providing a structural basis for the selectivity. In addition, YD1113 can be modified by introducing a substrate mimic to form a "T-shaped" bisubstrate analogue YD1290 to engage both the SAM and substrate binding pockets, exhibiting potent and selective inhibition to type I PRMTs (IC 50  < 5 nmol/L). In summary, we demonstrated the promise of YD1113 as a general SAH mimic to build potent and selective PRMT inhibitors.


  • Organizational Affiliation

    Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research, Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein arginine N-methyltransferase 3340Homo sapiensMutation(s): 0 
Gene Names: PRMT3HRMT1L3
EC: 2.1.1.319
UniProt & NIH Common Fund Data Resources
Find proteins for O60678 (Homo sapiens)
Explore O60678 
Go to UniProtKB:  O60678
PHAROS:  O60678
GTEx:  ENSG00000185238 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60678
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DVS (Subject of Investigation/LOI)
Query on DVS

Download Ideal Coordinates CCD File 
B [auth A]5'-S-[3-(N'-benzylcarbamimidamido)propyl]-5'-thioadenosine
C21 H28 N8 O3 S
LTPOXWXTHQVJKG-WVSUBDOOSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.733α = 90
b = 70.733β = 90
c = 175.262γ = 90
Software Package:
Software NamePurpose
HKL-3000data scaling
PHASERphasing
REFMACrefinement
HKL-3000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateCanada--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Data collection, Database references