5CCL

Crystal structure of SMYD3 with SAM and oxindole compound

• PDB DOI: https://doi.org/10.2210/pdb5CCL/pdb

• Classification: TRANSFERASE/TRANSFERASE Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.164 
• R-Value Work: 0.113 
• R-Value Observed: 0.116 

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

• PubMed: 26985287 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.85 kDa 
• Atom Count: 4,170 
• Modelled Residue Count: 425 
• Deposited Residue Count: 432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase SMYD3	A	432	Homo sapiens	Mutation(s): 0  Gene Names: SMYD3, ZMYND1, ZNFN3A1 EC: 2.1.1.43
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H7B4 (Homo sapiens) Explore Q9H7B4  Go to UniProtKB:  Q9H7B4
PHAROS:  Q9H7B4 GTEx:  ENSG00000185420

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	E [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
4ZW	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	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.164 
• R-Value Work: 0.113 
• R-Value Observed: 0.116 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.594	α = 90
b = 65.232	β = 90
c = 105.966	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

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