Crystal structure of SMYD3 with SAM and EPZ030456

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


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: https://doi.org/10.1021/acsmedchemlett.5b00272
  • Primary Citation of Related Structures:  
    5CCL, 5CCM

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase SMYD3428Homo sapiensMutation(s): 0 
EC: (PDB Primary Data), (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H7B4 (Homo sapiens)
Explore Q9H7B4 
Go to UniProtKB:  Q9H7B4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H7B4
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
4ZX Binding MOAD:  5CCM IC50: 4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.484α = 90
b = 65.852β = 90
c = 107.358γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

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