5CCM | pdb_00005ccm

Crystal structure of SMYD3 with SAM and EPZ030456

• PDB DOI: https://doi.org/10.2210/pdb5CCM/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: 2.30 Å
• R-Value Free: 
  0.255 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

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 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: 50.32 kDa 
• Atom Count: 3,582 
• Modeled Residue Count: 423 
• Deposited Residue Count: 428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase SMYD3	A	428	Homo sapiens	Mutation(s): 0  Gene Names: SMYD3, ZMYND1, ZNFN3A1 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4ZX	F [auth A]	6-chloranyl-2-oxidanylidene-N-[(1S,5R)-8-[4-[(phenylmethyl)amino]piperidin-1-yl]sulfonyl-8-azabicyclo[3.2.1]octan-3-yl]-1,3-dihydroindole-5-carboxamide C28 H34 Cl N5 O4 S SSDPURPCLGSTBN-NUNAXRQHSA-N
SAM	E [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4ZX	BindingDB:  5CCM	Ki: min: 1.3, max: 4.7 (nM) from 2 assay(s)
		IC50: min: 2.58, max: 48 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.255 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.484	α = 90
b = 65.852	β = 90
c = 107.358	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