4RYL

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 10.1002/anie.201412154
  • Structures With Same Primary Citation

  • 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 ...

    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).



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PRMT3 proteinA340Homo sapiensMutation(s): 0 
Gene Names: PRMT3HRMT1L3
EC: 2.1.1
Find proteins for O60678 (Homo sapiens)
Explore O60678 
Go to UniProtKB:  O60678
NIH Common Fund Data Resources
PHAROS  O60678
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3ZG
Query on 3ZG

Download CCD File 
A
1-isoquinolin-6-yl-3-[2-oxo-2-(pyrrolidin-1-yl)ethyl]urea
C16 H18 N4 O2
DMIDPTCQPIJYFE-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download CCD File 
A
UNKNOWN ATOM OR ION
X
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3ZGIC50:  31   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
PDB_EXTRACTdata extraction
JDirectordata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • 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