5ARG

SMYD2 in complex with SGC probe BAY-598


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Discovery and Characterization of a Highly Potent and Selective Aminopyrazoline-Based in Vivo Probe (Bay-598) for the Protein Lysine Methyltransferase Smyd2.

Eggert, E.Hillig, R.C.Kohr, S.Stockigt, D.Weiske, J.Barak, N.Mowat, J.Brumby, T.Christ, C.D.Ter Laak, A.Lang, T.Fernandez-Montalvan, A.E.Badock, V.Weinmann, H.Hartung, I.V.Barsyte-Lovejoy, D.Szewczyk, M.Kennedy, S.Li, F.Vedadi, M.Brown, P.J.Santhakumar, V.Arrowsmith, C.H.Stellfeld, T.Stresemann, C.

(2016) J.Med.Chem. 59: 4578

  • DOI: 10.1021/acs.jmedchem.5b01890
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protein lysine methyltransferases have recently emerged as a new target class for the development of inhibitors that modulate gene transcription or signaling pathways. SET and MYND domain containing protein 2 (SMYD2) is a catalytic SET domain contain ...

    Protein lysine methyltransferases have recently emerged as a new target class for the development of inhibitors that modulate gene transcription or signaling pathways. SET and MYND domain containing protein 2 (SMYD2) is a catalytic SET domain containing methyltransferase reported to monomethylate lysine residues on histone and nonhistone proteins. Although several studies have uncovered an important role of SMYD2 in promoting cancer by protein methylation, the biology of SMYD2 is far from being fully understood. Utilization of highly potent and selective chemical probes for target validation has emerged as a concept which circumvents possible limitations of knockdown experiments and, in particular, could result in an improved exploration of drug targets with a complex underlying biology. Here, we report the development of a potent, selective, and cell-active, substrate-competitive inhibitor of SMYD2, which is the first reported inhibitor suitable for in vivo target validation studies in rodents.


    Organizational Affiliation

    Drug Discovery, BAYER Pharma AG , Muellerstrasse 178, 13353 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-LYSINE METHYLTRANSFERASE SMYD2
A
433Homo sapiensMutation(s): 0 
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 4 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
H41
Query on H41

Download SDF File 
Download CCD File 
A
N-[1-(N'-CYANO-N-[3-(DIFLUOROMETHOXY)PHENYL]CARBAMIMIDOYL)-3-(3,4-DICHLOROPHENYL)-4,5-DIHYDRO-1H-PYRAZOL-4-YL]-N-ETHYL-2-HYDROXYACETAMIDE
C22 H20 Cl2 F2 N6 O3
OTTJIRVZJJGFTK-SFHVURJKSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
H41IC50: 27 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.343α = 90.00
b = 69.600β = 90.00
c = 131.115γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-06-08
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Data collection
  • Version 1.3: 2019-04-03
    Type: Data collection, Experimental preparation