Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.74 kDa 
• Atom Count: 2,577 
• Modelled Residue Count: 299 
• Deposited Residue Count: 340 
• Unique protein chains: 1

 4QQN

Protein arginine methyltransferase 3 in complex with compound MTV044246

• PDB DOI: 10.2210/pdb4QQN/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-06-27 Released: 2014-09-17 
• Deposition Author(s): Dong, A., Dobrovetsky, E., Tempel, W., He, H., Zhao, K., Smil, D., Landon, M., Luo, X., Chen, Z., Dai, M., Yu, Z., Lin, Y., Zhang, H., Zhao, K., Schapira, M., Brown, P.J., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Vedadi, M., Structural Genomics Consortium (SGC)

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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 

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

• PubMed: 29244490 
• 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. 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PRMT3 protein	A	340	Homo sapiens	Mutation(s): 0  Gene Names: PRMT3, HRMT1L3 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3BQ	B [auth A]	1-{2-[1-(aminomethyl)cyclohexyl]ethyl}-3-isoquinolin-6-ylurea C19 H26 N4 O NYAKHMNXWJGORW-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNX	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

Binding Affinity Annotations
ID	Source	Binding 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 = 70.319	α = 90
b = 70.319	β = 90
c = 172.918	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-17 
Deposition Author(s): Dong, A., Dobrovetsky, E., Tempel, W., He, H., Zhao, K., Smil, D., Landon, M., Luo, X., Chen, Z., Dai, M., Yu, Z., Lin, Y., Zhang, H., Zhao, K., Schapira, M., Brown, P.J., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Vedadi, M., Structural Genomics Consortium (SGC)

Revision History  

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