Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 38.58 kDa 
• Atom Count: 2582 
• Modelled Residue Count: 300 
• Deposited Residue Count: 340 
• Unique protein chains: 1

4RYL

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

• PDB DOI: 10.2210/pdb4RYL/pdb

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


• Deposited: 2014-12-15 Released: 2015-02-25 
• Deposition Author(s): Dong, A., Dobrovetsky, E., Kaniskan, H.U., Szewczyk, M., Yu, Z., Eram, M.S., Yang, X., Schmidt, K., Luo, X., Dai, M., He, F., Zang, I., Lin, Y., Kennedy, S., Li, F., Tempel, W., Smil, D., Min, S.J., Landon, M., Lin-Jones, J., Huang, X.P., Roth, B.L., Schapira, M., Atadja, P., Barsyte-Lovejoy, D., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Brown, P.J., Zhao, K., Jin, J., Vedadi, M., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

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

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

• PubMed: 25728001 
• DOI: 10.1002/anie.201412154
• Primary Citation of Related Structures:  
  4RYL


• 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.

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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

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
UniProt & NIH Common Fund Data Resources
Find proteins for O60678 (Homo sapiens) Explore O60678  Go to UniProtKB:  O60678
PHAROS:  O60678

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3ZG	B [auth A]	1-isoquinolin-6-yl-3-[2-oxo-2-(pyrrolidin-1-yl)ethyl]urea C16 H18 N4 O2 DMIDPTCQPIJYFE-UHFFFAOYSA-N
UNX	C [auth A], D [auth A]	UNKNOWN ATOM OR ION X

Binding Affinity Annotations
ID	Source	Binding 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

• 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 = 70.691	α = 90
b = 70.691	β = 90
c = 173.559	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-12-15 
• Released Date: 2015-02-25 
Deposition Author(s): Dong, A., Dobrovetsky, E., Kaniskan, H.U., Szewczyk, M., Yu, Z., Eram, M.S., Yang, X., Schmidt, K., Luo, X., Dai, M., He, F., Zang, I., Lin, Y., Kennedy, S., Li, F., Tempel, W., Smil, D., Min, S.J., Landon, M., Lin-Jones, J., Huang, X.P., Roth, B.L., Schapira, M., Atadja, P., Barsyte-Lovejoy, D., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Brown, P.J., Zhao, K., Jin, J., Vedadi, M., Structural Genomics Consortium (SGC)

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