5CCL | pdb_00005ccl

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.164 (Depositor), 0.165 (DCC)
R-Value Work:
0.113 (Depositor), 0.113 (DCC)
R-Value Observed:
0.116 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

PubMed: 26985287 Search on PubMed Search on PubMed Central
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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 (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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H7B4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
4ZW Query on 4ZW Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	2-oxidanylidene-N-piperidin-4-yl-1,3-dihydroindole-5-carboxamide C₁₄ H₁₇ N₃ O₂ SWMKOYKJOHHEQD-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Binding Affinity Annotations
ID	Source	Binding 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), 0.165 (DCC)
R-Value Work: 0.113 (Depositor), 0.113 (DCC)
R-Value Observed: 0.116 (Depositor)

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

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-09-09

Deposition Author(s):

Boriack-Sjodin, P.A.

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