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: 42.93 kDa 
• Atom Count: 2,750 
• Modelled Residue Count: 328 
• Deposited Residue Count: 376 
• Unique protein chains: 1

 6W6D

Crystal Structure of Human Protein arginine N-methyltransferase 6 (PRMT6) in complex with SGC6870 inhibitor

• PDB DOI: 10.2210/pdb6W6D/pdb

• Classification: TRANSFERASE/TRANSFERASE Inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2020-03-16 Released: 2020-04-29 
• Deposition Author(s): Halabelian, L., Zeng, H., Dong, A., Jin, J., Shen, Y., Kaniskan, H.U., Hutchinson, A., Seitova, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Brown, P.J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.209 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 

Literature

A First-in-Class, Highly Selective and Cell-Active Allosteric Inhibitor of Protein Arginine Methyltransferase 6.

Shen, Y., Li, F., Szewczyk, M.M., Halabelian, L., Chau, I., Eram, M.S., Dela Sena, C., Park, K.S., Meng, F., Chen, H., Zeng, H., Dong, A., Wu, H., Trush, V.V., McLeod, D., Zepeda-Velazquez, C.A., Campbell, R.M., Mader, M.M., Watson, B.M., Schapira, M., Arrowsmith, C.H., Al-Awar, R., Barsyte-Lovejoy, D., Kaniskan, H.U., Brown, P.J., Vedadi, M., Jin, J.

(2021) J Med Chem 64: 3697-3706

• PubMed: 33591753 
• DOI: 10.1021/acs.jmedchem.0c02160
• Primary Citation of Related Structures:  
  6W6D


• PubMed Abstract: 
  

Protein arginine methyltransferase 6 (PRMT6) catalyzes monomethylation and asymmetric dimethylation of arginine residues in various proteins, plays important roles in biological processes, and is associated with multiple cancers. To date, a highly selective PRMT6 inhibitor has not been reported. Here we report the discovery and characterization of a first-in-class, highly selective allosteric inhibitor of PRMT6, (R)- 2 (SGC6870). (R)- 2 is a potent PRMT6 inhibitor (IC ₅₀ = 77 ± 6 nM) with outstanding selectivity for PRMT6 over a broad panel of other methyltransferases and nonepigenetic targets. Notably, the crystal structure of the PRMT6- (R)- 2 complex and kinetic studies revealed (R)- 2 binds a unique, induced allosteric pocket. Additionally, (R)- 2 engages PRMT6 and potently inhibits its methyltransferase activity in cells. Moreover, (R)- 2 's enantiomer, (S)- 2 (SGC6870N), is inactive against PRMT6 and can be utilized as a negative control. Collectively, (R) - 2 is a well-characterized PRMT6 chemical probe and a valuable tool for further investigating PRMT6 functions in health and disease.

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Organizational Affiliation: 

Mount Sinai Center for Therapeutics 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
Protein arginine N-methyltransferase 6	A	376	Homo sapiens	Mutation(s): 0  Gene Names: PRMT6, HRMT1L6 EC: 2.1.1.319
UniProt & NIH Common Fund Data Resources
Find proteins for Q96LA8 (Homo sapiens) Explore Q96LA8  Go to UniProtKB:  Q96LA8
PHAROS:  Q96LA8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T9A (Subject of Investigation/LOI)	C [auth A]	(5R)-4-(5-bromothiophene-2-carbonyl)-5-(3,5-dimethylphenyl)-7-methyl-1,3,4,5-tetrahydro-2H-1,4-benzodiazepin-2-one C23 H21 Br N2 O2 S NIPTUMFVYBXSMZ-JOCHJYFZSA-N
SAH	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.209 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 
• Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.603	α = 90
b = 94.603	β = 90
c = 108.094	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-29 
Deposition Author(s): Halabelian, L., Zeng, H., Dong, A., Jin, J., Shen, Y., Kaniskan, H.U., Hutchinson, A., Seitova, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Brown, P.J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2020-04-29
  Type: Initial release
  
• Version 1.1: 2022-02-23
  Changes: Database references