5KJN

SMYD2 in complex with AZ506


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Design, Synthesis, and Biological Activity of Substrate Competitive SMYD2 Inhibitors.

Cowen, S.D.Russell, D.Dakin, L.A.Chen, H.Larsen, N.A.Godin, R.Throner, S.Zheng, X.Molina, A.Wu, J.Cheung, T.Howard, T.Garcia-Arenas, R.Keen, N.Pendleton, C.S.Pietenpol, J.A.Ferguson, A.D.

(2016) J. Med. Chem. 59: 11079-11097

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protein lysine methyltransferases (KMTs) have emerged as important regulators of epigenetic signaling. These enzymes catalyze the transfer of donor methyl groups from the cofactor S-adenosylmethionine to specific acceptor lysine residues on histones, ...

    Protein lysine methyltransferases (KMTs) have emerged as important regulators of epigenetic signaling. These enzymes catalyze the transfer of donor methyl groups from the cofactor S-adenosylmethionine to specific acceptor lysine residues on histones, leading to changes in chromatin structure and transcriptional regulation. These enzymes also methylate an array of nonhistone proteins, suggesting additional mechanisms by which they influence cellular physiology. SMYD2 is reported to be an oncogenic methyltransferase that represses the functional activity of the tumor suppressor proteins p53 and RB. HTS screening led to identification of five distinct substrate-competitive chemical series. Determination of liganded crystal structures of SMYD2 contributed significantly to "hit-to-lead" design efforts, culminating in the creation of potent and selective inhibitors that were used to understand the functional consequences of SMYD2 inhibition. Taken together, these results have broad implications for inhibitor design against KMTs and clearly demonstrate the potential for developing novel therapies against these enzymes.


    Organizational Affiliation

    Department of Biochemistry, Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville, Tennessee 37232 United States.,Structure and Biophysics, Discovery Sciences, AstraZeneca, Mereside , Alderley Park, Cheshire, SK10 4TG United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-lysine methyltransferase SMYD2
A
429Homo sapiensMutation(s): 1 
Gene Names: SMYD2 (KMT3C)
EC: 2.1.1.-
Find proteins for Q9NRG4 (Homo sapiens)
Go to Gene View: SMYD2
Go to UniProtKB:  Q9NRG4
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
BU3
Query on BU3

Download SDF File 
Download CCD File 
A
(R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
 Ligand Interaction
6TL
Query on 6TL

Download SDF File 
Download CCD File 
A
5-[2-[4-[2-(1~{H}-indol-3-yl)ethyl]piperazin-1-yl]phenyl]-~{N}-(3-pyrrolidin-1-ylpropyl)pyridine-3-carboxamide
AZ506
C33 H40 N6 O
VCPDGNYFXJYJFB-UHFFFAOYSA-N
 Ligand Interaction
SAM
Query on SAM

Download SDF File 
Download CCD File 
A
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.162 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 154.871α = 90.00
b = 154.871β = 90.00
c = 52.286γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTERrefinement
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-06-20 
  • Released Date: 2016-12-07 
  • Deposition Author(s): Ferguson, A.

Revision History 

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2017-01-04
    Type: Database references