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


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/acschembio.5b00839
  • Primary Citation of Related Structures:  
    5E8R

  • 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 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

    Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
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)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96LA8 (Homo sapiens)
Explore Q96LA8 
Go to UniProtKB:  Q96LA8
PHAROS:  Q96LA8
GTEx:  ENSG00000198890 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96LA8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
5L6
Query on 5L6

Download Ideal Coordinates CCD File 
D [auth A],
H [auth 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
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNX
Query on UNX

Download Ideal Coordinates CCD File 
F [auth A]
M [auth B]
N [auth B]
O [auth B]
P [auth B]
F [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B]
UNKNOWN ATOM OR ION
X
Binding Affinity Annotations 
IDSourceBinding Affinity
5L6 BindingDB:  5E8R Ki: 0.8 (nM) from 1 assay(s)
Kd: 6 (nM) from 1 assay(s)
IC50: 4 (nM) from 1 assay(s)
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



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references