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.

Macromolecule Content

• Total Structure Weight: 50852.25 
• Atom Count: 3548 
• Residue Count: 429 
• Unique protein chains: 1

5KJK

SMYD2 in complex with AZ370

• DOI: 10.2210/pdb5KJK/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.203 
• R-Value Work: 0.178 

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

• PubMed: 28002961 
• Primary Citation of Related Structures:  
  5KJN, 5KJM, 5KJL


• 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, 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.

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Organizational Affiliation: 

Structure and Biophysics, Discovery Sciences, AstraZeneca, Mereside , Alderley Park, Cheshire, SK10 4TG United Kingdom.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
N-lysine methyltransferase SMYD2	A	429	Homo sapiens	Mutation(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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
BU3	A	(R,R)-2,3-BUTANEDIOL C4 H10 O2 OWBTYPJTUOEWEK-QWWZWVQMSA-N
6T1	A	2-[2-[1-[2-(3,4-dichlorophenyl)ethyl]azetidin-3-yl]oxyphenyl]-~{N}-(3-pyrrolidin-1-ylpropyl)pyridine-4-carboxamide AZ13450370 C30 H34 Cl2 N4 O2 AGSYPSPYUHOIIZ-UHFFFAOYSA-N
SAM	A	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
6T1	IC50: 12 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.203 
• R-Value Work: 0.178 
• Space Group: I 4

Unit Cell:

Length (Å)	Angle (°)
a = 155.865	α = 90.00
b = 155.865	β = 90.00
c = 52.477	γ = 90.00

Software Package:

Software Name	Purpose
MOLREP	phasing
XDS	data reduction
BUSTER	refinement
SCALA	data scaling

Structure Validation

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