5CCL | pdb_00005ccl

Crystal structure of SMYD3 with SAM and oxindole compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.164 (Depositor), 0.160 (DCC) 
  • R-Value Work: 
    0.113 (Depositor), 0.110 (DCC) 
  • R-Value Observed: 
    0.116 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SAMClick on this verticalbar to view detailsBest fitted 4ZWClick on this verticalbar to view details

This is version 1.2 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: 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase SMYD3432Homo sapiensMutation(s): 0 
Gene Names: SMYD3ZMYND1ZNFN3A1
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.354 (UniProt)
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 
E [auth A]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
4ZW
Query on 4ZW

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
2-oxidanylidene-N-piperidin-4-yl-1,3-dihydroindole-5-carboxamide
C14 H17 N3 O2
SWMKOYKJOHHEQD-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
4ZW BindingDB:  5CCL IC50: min: 1.00e+4, max: 1.70e+4 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.164 (Depositor), 0.160 (DCC) 
  • R-Value Work:  0.113 (Depositor), 0.110 (DCC) 
  • R-Value Observed: 0.116 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.594α = 90
b = 65.232β = 90
c = 105.966γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SAMClick on this verticalbar to view detailsBest fitted 4ZWClick on this verticalbar to view details

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
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Derived calculations