6W6D

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


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein arginine N-methyltransferase 6A376Homo sapiensMutation(s): 0 
Gene Names: PRMT6HRMT1L6
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96LA8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / 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
NIPTUMFVYBXSMZ-JOCHJYFZSA-N
 Ligand Interaction
SAH
Query on SAH

Download Ideal Coordinates CCD File 
B [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
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 = 94.603α = 90
b = 94.603β = 90
c = 108.094γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
REFMACphasing

Structure Validation

View Full Validation Report



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