6YUH

Crystal structure of SMYD3 with diperodon R enantiomer bound to allosteric site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase.

Talibov, V.O.Fabini, E.FitzGerald, E.A.Tedesco, D.Cederfeldt, D.Talu, M.J.Rachman, M.M.Mihalic, F.Manoni, E.Naldi, M.Sanese, P.Forte, G.Lepore Signorile, M.Barril, X.Simone, C.Bartolini, M.Dobritzsch, D.Del Rio, A.Danielson, U.H.

(2021) Chembiochem 22: 1597-1608

  • DOI: https://doi.org/10.1002/cbic.202000736
  • Primary Citation of Related Structures:  
    6YUH

  • PubMed Abstract: 

    SMYD3 is a multifunctional epigenetic enzyme with lysine methyltransferase activity and various interaction partners. It is implicated in the pathophysiology of cancers but with an unclear mechanism. To discover tool compounds for clarifying its biochemistry and potential as a therapeutic target, a set of drug-like compounds was screened in a biosensor-based competition assay. Diperodon was identified as an allosteric ligand; its R and S enantiomers were isolated, and their affinities to SMYD3 were determined (K D =42 and 84 μM, respectively). Co-crystallization revealed that both enantiomers bind to a previously unidentified allosteric site in the C-terminal protein binding domain, consistent with its weak inhibitory effect. No competition between diperodon and HSP90 (a known SMYD3 interaction partner) was observed although SMYD3-HSP90 binding was confirmed (K D =13 μM). Diperodon clearly represents a novel starting point for the design of tool compounds interacting with a druggable allosteric site, suitable for the exploration of noncatalytic SMYD3 functions and therapeutics with new mechanisms of action.


  • Organizational Affiliation

    Department of Chemistry-BMC, Uppsala University, Husargatan 3, 754 24, Uppsala, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase SMYD3425Homo sapiensMutation(s): 0 
Gene Names: SMYD3ZMYND1ZNFN3A1
EC: 2.1.1.354
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H7B4 (Homo sapiens)
Explore Q9H7B4 
Go to UniProtKB:  Q9H7B4
PHAROS:  Q9H7B4
GTEx:  ENSG00000185420 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H7B4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download Ideal Coordinates CCD File 
B [auth A]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
POW (Subject of Investigation/LOI)
Query on POW

Download Ideal Coordinates CCD File 
D [auth A]Diperodon
C22 H27 N3 O4
YUGZHQHSNYIFLG-HXUWFJFHSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
H [auth A],
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.142α = 90
b = 66.284β = 90
c = 105.949γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSwedenD0571301
Italian Association for Cancer ResearchItaly19172

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-05-12
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description