6P6K | pdb_00006p6k

Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors

PDB DOI: https://doi.org/10.2210/pdb6P6K/pdb

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

Deposited: 2019-06-04 Released: 2020-01-15
Deposition Author(s): Elkins, P.A., Wang, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.214 (Depositor), 0.215 (DCC)
R-Value Work:
0.178 (Depositor), 0.179 (DCC)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Discovery of Isoxazole Amides as Potent and Selective SMYD3 Inhibitors.

Su, D.S., Qu, J., Schulz, M., Blackledge, C.W., Yu, H., Zeng, J., Burgess, J., Reif, A., Stern, M., Nagarajan, R., Pappalardi, M.B., Wong, K., Graves, A.P., Bonnette, W., Wang, L., Elkins, P., Knapp-Reed, B., Carson, J.D., McHugh, C., Mohammad, H., Kruger, R., Luengo, J., Heerding, D.A., Creasy, C.L.

(2020) ACS Med Chem Lett 11: 133-140

PubMed: 32071679 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.9b00493
Primary Citation Related Structures:
6P6G, 6P6K, 6P7Z, 6PAF

PubMed Abstract:
We report herein the discovery of isoxazole amides as potent and selective SET and MYND Domain-Containing Protein 3 (SMYD3) inhibitors. Elucidation of the structure-activity relationship of the high-throughput screening (HTS) lead compound 1 provided potent and selective SMYD3 inhibitors. The SAR optimization, cocrystal structures of small molecules with SMYD3, and mode of inhibition (MOI) characterization of compounds are described. The synthesis and biological and pharmacokinetic profiles of compounds are also presented.

Organizational Affiliation

Medicinal Chemistry, Medicine Design, Oncology R&D, Data and Computational Sciences, and Protein Cellular and Structural Sciences, Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States.

Macromolecule Content

Total Structure Weight: 50.59 kDa
Atom Count: 3,832
Modeled Residue Count: 424
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM 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]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
L0J (Subject of Investigation/LOI) Query on L0J Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	N-{1-[(2-aminoethyl)sulfonyl]piperidin-4-yl}-5-cyclopropyl-1,2-oxazole-3-carboxamide C₁₄ H₂₂ N₄ O₄ S AMCHZZBLDUVCGF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [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 G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
L0J	BindingDB: 6P6K	IC50: min: 398, max: 1421 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.214 (Depositor), 0.215 (DCC)
R-Value Work: 0.178 (Depositor), 0.179 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.719	α = 90
b = 66.038	β = 90
c = 105.773	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-01-15

Deposition Author(s):

Elkins, P.A.

Wang, L.

Revision History (Full details and data files)

Version 1.0: 2020-01-15
Type: Initial release
Version 1.1: 2020-03-11
Changes: Database references
Version 1.2: 2024-03-13
Changes: Data collection, Database references, Derived calculations