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


Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    4QQN

  • 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 inhibitor of PRMT3, compound 4 ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PRMT3 proteinA340Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60678
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3BQ
Query on 3BQ

Download Ideal Coordinates CCD File 
B [auth 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 Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
UNX
Query on UNX

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [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]
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
3BQ BindingDB:  4QQN IC50: 291 (nM) from 1 assay(s)
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



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

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