6ZRB | pdb_00006zrb

Crystal structure of SMYD3 conjugate with piperidine-based covalent inhibitor EM127

PDB DOI: https://doi.org/10.2210/pdb6ZRB/pdb

Classification: ONCOPROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-07-13 Released: 2022-07-27
Deposition Author(s): Talibov, V.O., Eriksson, D.
Funding Organization(s): Italian Association for Cancer Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.184 (Depositor), 0.196 (DCC)
R-Value Work:
0.165 (Depositor), 0.176 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Discovery of the 4-aminopiperidine-based compound EM127 for the site-specific covalent inhibition of SMYD3

Parenti, M.D., Naldi, M., Manoni, E., Fabini, E., Cederfelt, D., Talibov, V.O., Gressani, V., Guven, U., Grossi, V., Fasano, C., Sanese, P., De Marco, K., Shtil, A.A., Kurkin, A.V., Altieri, A., Danielson, U.H., Caretti, G., Simone, C., Varchi, G., Bartolini, M., Del Rio, A.

(2022) Eur J Med Chem : 114683

DOI: https://doi.org/10.1016/j.ejmech.2022.114683

Macromolecule Content

Total Structure Weight: 50.43 kDa
Atom Count: 3,883
Modeled Residue Count: 425
Deposited Residue Count: 431
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	431	Homo sapiens	Mutation(s): 2 Gene Names: SMYD3, ZMYND1, ZNFN3A1 EC: 2.1.1.354
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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
QON Query on QON Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	N-[1-(2-Chloroacetyl)piperidin-4-yl]-5-cyclopropyl-1,2-oxazole-3-carboxamide C₁₄ H₁₈ Cl N₃ O₃ OENTXAYVUCLRJQ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
QON	BindingDB: 6ZRB	Ki: 6110 (nM) from 1 assay(s)
		Kd: 1.30e+4 (nM) from 1 assay(s)
		IC50: min: 370, max: 3.35e+4 (nM) from 2 assay(s)