4WUY

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-lysine methyltransferase SMYD2 A441Homo sapiensMutation(s): 0 
Gene Names: SMYD2KMT3C
EC: 2.1.1 (PDB Primary Data), 2.1.1.43 (PDB Primary Data), 2.1.1.354 (UniProt)
Find proteins for Q9NRG4 (Homo sapiens)
Explore Q9NRG4 
Go to UniProtKB:  Q9NRG4
NIH Common Fund Data Resources
PHAROS:  Q9NRG4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3UJ
Query on 3UJ

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
SAH
Query on SAH

Download Ideal Coordinates CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SAHIC50:  180   nM  BindingDB
3UJIC50:  388   nM  BindingDB
3UJIC50:  15   nM  Binding MOAD
3UJIC50:  15   nM  BindingDB
3UJIC50:  600   nM  BindingDB
3UJIC50:  1000   nM  BindingDB
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 = 89.025α = 90
b = 99.92β = 90
c = 60.297γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • 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