5E8R

Human HMT1 hnRNP methyltransferase-like protein 6 (S. cerevisiae)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A Potent, Selective, and Cell-Active Inhibitor of Human Type I Protein Arginine Methyltransferases.

Eram, M.S.Shen, Y.Szewczyk, M.M.Wu, H.Senisterra, G.Li, F.Butler, K.V.Kaniskan, H.U.Speed, B.A.Dela Sena, C.Dong, A.Zeng, H.Schapira, M.Brown, P.J.Arrowsmith, C.H.Barsyte-Lovejoy, D.Liu, J.Vedadi, M.Jin, J.

(2016) ACS Chem Biol 11: 772-781

  • DOI: 10.1021/acschembio.5b00839
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Protein arginine methyltransferases (PRMTs) play a crucial role in a variety of biological processes. Overexpression of PRMTs has been implicated in various human diseases including cancer. Consequently, selective small-molecule inhibitors of PRMTs h ...

    Protein arginine methyltransferases (PRMTs) play a crucial role in a variety of biological processes. Overexpression of PRMTs has been implicated in various human diseases including cancer. Consequently, selective small-molecule inhibitors of PRMTs have been pursued by both academia and the pharmaceutical industry as chemical tools for testing biological and therapeutic hypotheses. PRMTs are divided into three categories: type I PRMTs which catalyze mono- and asymmetric dimethylation of arginine residues, type II PRMTs which catalyze mono- and symmetric dimethylation of arginine residues, and type III PRMT which catalyzes only monomethylation of arginine residues. Here, we report the discovery of a potent, selective, and cell-active inhibitor of human type I PRMTs, MS023, and characterization of this inhibitor in a battery of biochemical, biophysical, and cellular assays. MS023 displayed high potency for type I PRMTs including PRMT1, -3, -4, -6, and -8 but was completely inactive against type II and type III PRMTs, protein lysine methyltransferases and DNA methyltransferases. A crystal structure of PRMT6 in complex with MS023 revealed that MS023 binds the substrate binding site. MS023 potently decreased cellular levels of histone arginine asymmetric dimethylation. It also reduced global levels of arginine asymmetric dimethylation and concurrently increased levels of arginine monomethylation and symmetric dimethylation in cells. We also developed MS094, a close analog of MS023, which was inactive in biochemical and cellular assays, as a negative control for chemical biology studies. MS023 and MS094 are useful chemical tools for investigating the role of type I PRMTs in health and disease.


    Organizational Affiliation

    Departments of Structural and Chemical Biology, Oncological Sciences, and Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein arginine N-methyltransferase 6
A, B
376Homo sapiensMutation(s): 0 
Gene Names: PRMT6HRMT1L6
EC: 2.1.1 (PDB Primary Data), 2.1.1.125 (PDB Primary Data), 2.1.1.319 (UniProt)
Find proteins for Q96LA8 (Homo sapiens)
Go to UniProtKB:  Q96LA8
NIH Common Fund Data Resources
PHAROS  Q96LA8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
5L6
Query on 5L6

Download CCD File 
A, B
N-methyl-N-({4-[4-(propan-2-yloxy)phenyl]-1H-pyrrol-3-yl}methyl)ethane-1,2-diamine
C17 H25 N3 O
FMTVWAGUJRUAKE-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
UNX
Query on UNX

Download CCD File 
A, B
UNKNOWN ATOM OR ION
X
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5L6IC50:  4   nM  BindingDB
5L6Ki:  0.800000011920929   nM  BindingDB
5L6Kd:  6   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.244α = 90
b = 100.244β = 90
c = 89.868γ = 90
Software Package:
Software NamePurpose
HKL-3000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-09
    Type: Initial release
  • Version 1.1: 2016-03-30
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Derived calculations, Structure summary