Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50898.05 
• Atom Count: 3543 
• Residue Count: 433 
• Unique protein chains: 1

5ARG

SMYD2 in complex with SGC probe BAY-598

• DOI: 10.2210/pdb5ARG/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda


• Deposited: 2015-09-24 Released: 2016-04-27 
• Deposition Author(s): Hillig, R.C., Badock, V., Barak, N., Stellfeld, T., Eggert, E., ter Laak, A., Weiske, J., Christ, C.D., Koehr, S., Stoeckigt, D., Mowat, J., Mueller, T., Fernandez-Montalvan, A.E., Hartung, I.V., Stresemann, C., Brumby, T., Weinmann, H.

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Experimental Data Snapshot

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

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

• PubMed: 27075367 
• DOI: 10.1021/acs.jmedchem.5b01890
• Primary Citation of Related Structures:  
  5ARF


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
N-LYSINE METHYLTRANSFERASE SMYD2	A	433	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
H41	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
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
SAM	A	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
H41	IC50: 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 = 52.343	α = 90.00
b = 69.600	β = 90.00
c = 131.115	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data reduction
REFMAC	refinement
PHASER	phasing
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-09-24 
• Released Date: 2016-04-27 
• Deposition Author(s): Hillig, R.C., Badock, V., Barak, N., Stellfeld, T., Eggert, E., ter Laak, A., Weiske, J., Christ, C.D., Koehr, S., Stoeckigt, D., Mowat, J., Mueller, T., Fernandez-Montalvan, A.E., Hartung, I.V., Stresemann, C., Brumby, T., Weinmann, H.

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