4QQN

Protein arginine methyltransferase 3 in complex with compound MTV044246


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of Potent and Selective Allosteric Inhibitors of Protein Arginine Methyltransferase 3 (PRMT3).

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

(2018) J Med Chem 61: 1204-1217

  • DOI: 10.1021/acs.jmedchem.7b01674
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • PRMT3 catalyzes the asymmetric dimethylation of arginine residues of various proteins. It is crucial for maturation of ribosomes and has been implicated in several diseases. We recently disclosed a highly potent, selective, and cell-active allosteric ...

    PRMT3 catalyzes the asymmetric dimethylation of arginine residues of various proteins. It is crucial for maturation of ribosomes and has been implicated in several diseases. We recently disclosed a highly potent, selective, and cell-active allosteric inhibitor of PRMT3, compound 4. Here, we report comprehensive structure-activity relationship studies that target the allosteric binding site of PRMT3. We conducted design, synthesis, and evaluation of novel compounds in biochemical, selectivity, and cellular assays that culminated in the discovery of 4 and other highly potent (IC 50 values: ∼10-36 nM), selective, and cell-active allosteric inhibitors of PRMT3 (compounds 29, 30, 36, and 37). In addition, we generated compounds that are very close analogs of these potent inhibitors but displayed drastically reduced potency as negative controls (compounds 49-51). These inhibitors and negative controls are valuable chemical tools for the biomedical community to further investigate biological functions and disease associations of PRMT3.


    Organizational Affiliation

    Center for Chemical Biology and Drug Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States.



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
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3BQ
Query on 3BQ

Download CCD File 
A
1-{2-[1-(aminomethyl)cyclohexyl]ethyl}-3-isoquinolin-6-ylurea
C19 H26 N4 O
NYAKHMNXWJGORW-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
UNX
Query on UNX

Download CCD File 
A
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.319α = 90
b = 70.319β = 90
c = 172.918γ = 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



Entry History 

Revision History 

  • Version 1.0: 2014-09-17
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references