4WUY

Crystal Structure of Protein Lysine Methyltransferase SMYD2 in complex with LLY-507, a Cell-Active, Potent and Selective Inhibitor

• PDB DOI:  https://doi.org/10.2210/pdb4WUY/pdb

• Classification: Transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2014-11-04 Released: 2015-04-08 
• Deposition Author(s): Nguyen, H., Allali-Hassani, A., Antonysamy, S., Chang, S., Chen, L.H., Curtis, C., Emtage, S., Fan, L., Gheyi, T., Li, F., Liu, S., Martin, J.R., Mendel, D., Olsen, J.B., Pelletier, L., Shatseva, T., Wu, S., Zhang, F.F., Arrowsmith, C.H., Brown, P.J., Campbell, R.M., Garcia, B.A., Barsyte-Lovejoy, D., Mader, M., Vedadi, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.200 
• R-Value Work: 0.151 
• R-Value Observed: 0.154 

Literature

LLY-507, a Cell-active, Potent, and Selective Inhibitor of Protein-lysine Methyltransferase SMYD2.

Nguyen, H., Allali-Hassani, A., Antonysamy, S., Chang, S., Chen, L.H., Curtis, C., Emtage, S., Fan, L., Gheyi, T., Li, F., Liu, S., Martin, J.R., Mendel, D., Olsen, J.B., Pelletier, L., Shatseva, T., Wu, S., Zhang, F.F., Arrowsmith, C.H., Brown, P.J., Campbell, R.M., Garcia, B.A., Barsyte-Lovejoy, D., Mader, M., Vedadi, M.

(2015) J Biol Chem 290: 13641-13653

• PubMed: 25825497 
• DOI: https://doi.org/10.1074/jbc.M114.626861
• Primary Citation of Related Structures:  
  4WUY


• PubMed Abstract: 
  

SMYD2 is a lysine methyltransferase that catalyzes the monomethylation of several protein substrates including p53. SMYD2 is overexpressed in a significant percentage of esophageal squamous primary carcinomas, and that overexpression correlates with poor patient survival. However, the mechanism(s) by which SMYD2 promotes oncogenesis is not understood. A small molecule probe for SMYD2 would allow for the pharmacological dissection of this biology. In this report, we disclose LLY-507, a cell-active, potent small molecule inhibitor of SMYD2. LLY-507 is >100-fold selective for SMYD2 over a broad range of methyltransferase and non-methyltransferase targets. A 1.63-Å resolution crystal structure of SMYD2 in complex with LLY-507 shows the inhibitor binding in the substrate peptide binding pocket. LLY-507 is active in cells as measured by reduction of SMYD2-induced monomethylation of p53 Lys(370) at submicromolar concentrations. We used LLY-507 to further test other potential roles of SMYD2. Mass spectrometry-based proteomics showed that cellular global histone methylation levels were not significantly affected by SMYD2 inhibition with LLY-507, and subcellular fractionation studies indicate that SMYD2 is primarily cytoplasmic, suggesting that SMYD2 targets a very small subset of histones at specific chromatin loci and/or non-histone substrates. Breast and liver cancers were identified through in silico data mining as tumor types that display amplification and/or overexpression of SMYD2. LLY-507 inhibited the proliferation of several esophageal, liver, and breast cancer cell lines in a dose-dependent manner. These findings suggest that LLY-507 serves as a valuable chemical probe to aid in the dissection of SMYD2 function in cancer and other biological processes.

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Organizational Affiliation: 

Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower, 7th floor, Toronto, Ontario M5G 1L7, Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 52.27 kDa 
• Atom Count: 3,794 
• Modelled Residue Count: 414 
• Deposited Residue Count: 441 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-lysine methyltransferase SMYD2	A	441	Homo sapiens	Mutation(s): 0  Gene Names: SMYD2, KMT3C EC: 2.1.1 (PDB Primary Data), 2.1.1.43 (PDB Primary Data), 2.1.1.354 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRG4 (Homo sapiens) Explore Q9NRG4  Go to UniProtKB:  Q9NRG4
PHAROS:  Q9NRG4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3UJ	B [auth A]	5-cyano-2'-{4-[2-(3-methyl-1H-indol-1-yl)ethyl]piperazin-1-yl}-N-[3-(pyrrolidin-1-yl)propyl]biphenyl-3-carboxamide C36 H42 N6 O PNYRDVBFYVDJJI-UHFFFAOYSA-N
SAH	C [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
GOL	D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	G [auth A], H [auth A], I [auth A], J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3UJ	BindingDB:  4WUY	IC50: min: 15, max: 1000 (nM) from 5 assay(s)
	Binding MOAD:  4WUY	IC50: 15 (nM) from 1 assay(s)
SAH	BindingDB:  4WUY	IC50: 180 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.200 
• R-Value Work: 0.151 
• R-Value Observed: 0.154 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.025	α = 90
b = 99.92	β = 90
c = 60.297	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-08 
Deposition Author(s): Nguyen, H., Allali-Hassani, A., Antonysamy, S., Chang, S., Chen, L.H., Curtis, C., Emtage, S., Fan, L., Gheyi, T., Li, F., Liu, S., Martin, J.R., Mendel, D., Olsen, J.B., Pelletier, L., Shatseva, T., Wu, S., Zhang, F.F., Arrowsmith, C.H., Brown, P.J., Campbell, R.M., Garcia, B.A., Barsyte-Lovejoy, D., Mader, M., Vedadi, M.

Revision History  

• Version 1.0: 2015-04-08
  Type: Initial release
  
• Version 1.1: 2015-04-15
  Changes: Database references
• Version 1.2: 2015-06-10
  Changes: Database references