Human Protein Arginine Methyltransferase 3 in complex with 1-isoquinolin-6-yl-3-[2-oxo-2-(pyrrolidin-1-yl)ethyl]urea

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.186 

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This is version 1.4 of the entry. See complete history


A Potent, Selective and Cell-Active Allosteric Inhibitor of Protein Arginine Methyltransferase 3 (PRMT3).

Kaniskan, H.U.Szewczyk, M.M.Yu, Z.Eram, M.S.Yang, X.Schmidt, K.Luo, X.Dai, M.He, F.Zang, I.Lin, Y.Kennedy, S.Li, F.Dobrovetsky, E.Dong, A.Smil, D.Min, S.J.Landon, M.Lin-Jones, J.Huang, X.P.Roth, B.L.Schapira, M.Atadja, P.Barsyte-Lovejoy, D.Arrowsmith, C.H.Brown, P.J.Zhao, K.Jin, J.Vedadi, M.

(2015) Angew Chem Int Ed Engl 54: 5166-5170

  • DOI: https://doi.org/10.1002/anie.201412154
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    PRMT3 catalyzes the asymmetric dimethylation of arginine residues of various proteins. It is essential for maturation of ribosomes, may have a role in lipogenesis, and is implicated in several diseases. A potent, selective, and cell-active PRMT3 inhibitor would be a valuable tool for further investigating PRMT3 biology. Here we report the discovery of the first PRMT3 chemical probe, SGC707, by structure-based optimization of the allosteric PRMT3 inhibitors we reported previously, and thorough characterization of this probe in biochemical, biophysical, and cellular assays. SGC707 is a potent PRMT3 inhibitor (IC50 =31±2 nM, KD =53±2 nM) with outstanding selectivity (selective against 31 other methyltransferases and more than 250 non-epigenetic targets). The mechanism of action studies and crystal structure of the PRMT3-SGC707 complex confirm the allosteric inhibition mode. Importantly, SGC707 engages PRMT3 and potently inhibits its methyltransferase activity in cells. It is also bioavailable and suitable for animal studies. This well-characterized chemical probe is an excellent tool to further study the role of PRMT3 in health and disease.

  • Organizational Affiliation

    Departments of Structural and Chemical Biology, Oncological Sciences, and Pharmacology and System Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029 (USA).

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PRMT3 protein340Homo sapiensMutation(s): 0 
Gene Names: PRMT3
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
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
3ZG Binding MOAD:  4RYL Kd: 53 (nM) from 1 assay(s)
BindingDB:  4RYL IC50: min: 19, max: 225 (nM) from 3 assay(s)
EC50: min: 1800, max: 2000 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.186 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.691α = 90
b = 70.691β = 90
c = 173.559γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
JDirectordata collection
HKL-3000data reduction
HKL-3000data scaling
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 1.1: 2015-03-18
    Changes: Database references, Structure summary
  • Version 1.2: 2015-05-06
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description