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

Experimental Data Snapshot

  • Resolution: 1.91 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c02160
  • Primary Citation of Related Structures:  

  • 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.

  • 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein arginine N-methyltransferase 6376Homo sapiensMutation(s): 0 
Gene Names: PRMT6HRMT1L6
UniProt & NIH Common Fund Data Resources
Find proteins for Q96LA8 (Homo sapiens)
Explore Q96LA8 
Go to UniProtKB:  Q96LA8
GTEx:  ENSG00000198890 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96LA8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T9A (Subject of Investigation/LOI)
Query on T9A

Download Ideal Coordinates CCD File 
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
Query on SAH

Download Ideal Coordinates CCD File 
C14 H20 N6 O5 S
Experimental Data & Validation

Experimental Data

  • 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 = 94.603α = 90
b = 94.603β = 90
c = 108.094γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2022-02-23
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description