5CCL

Crystal structure of SMYD3 with SAM and oxindole compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.113 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Novel Oxindole Sulfonamides and Sulfamides: EPZ031686, the First Orally Bioavailable Small Molecule SMYD3 Inhibitor.

Mitchell, L.H.Boriack-Sjodin, P.A.Smith, S.Thomenius, M.Rioux, N.Munchhof, M.Mills, J.E.Klaus, C.Totman, J.Riera, T.V.Raimondi, A.Jacques, S.L.West, K.Foley, M.Waters, N.J.Kuntz, K.W.Wigle, T.J.Scott, M.P.Copeland, R.A.Smith, J.J.Chesworth, R.

(2016) Acs Med.Chem.Lett. 7: 134-138

  • DOI: 10.1021/acsmedchemlett.5b00272
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • SMYD3 has been implicated in a range of cancers; however, until now no potent selective small molecule inhibitors have been available for target validation studies. A novel oxindole series of SMYD3 inhibitors was identified through screening of the E ...

    SMYD3 has been implicated in a range of cancers; however, until now no potent selective small molecule inhibitors have been available for target validation studies. A novel oxindole series of SMYD3 inhibitors was identified through screening of the Epizyme proprietary histone methyltransferase-biased library. Potency optimization afforded two tool compounds, sulfonamide EPZ031686 and sulfamide EPZ030456, with cellular potency at a level sufficient to probe the in vitro biology of SMYD3 inhibition. EPZ031686 shows good bioavailability following oral dosing in mice making it a suitable tool for potential in vivo target validation studies.


    Organizational Affiliation

    Epizyme Inc. , Fourth Floor, 400 Technology Square, Cambridge, Massachusetts 02139, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase SMYD3
A
432Homo sapiensMutation(s): 0 
Gene Names: SMYD3 (ZMYND1, ZNFN3A1)
EC: 2.1.1.354
Find proteins for Q9H7B4 (Homo sapiens)
Go to Gene View: SMYD3
Go to UniProtKB:  Q9H7B4
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4ZW
Query on 4ZW

Download SDF File 
Download CCD File 
A
2-oxidanylidene-N-piperidin-4-yl-1,3-dihydroindole-5-carboxamide
C14 H17 N3 O2
SWMKOYKJOHHEQD-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
SAM
Query on SAM

Download SDF File 
Download CCD File 
A
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.113 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.594α = 90.00
b = 65.232β = 90.00
c = 105.966γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-07-02 
  • Released Date: 2015-09-09 
  • Deposition Author(s): Boriack-Sjodin, P.A.

Revision History 

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2016-03-30
    Type: Database references