6ZRB

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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.184 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

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

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration, mass spectrometry

Macromolecule Content

• Total Structure Weight: 50.43 kDa 
• Atom Count: 3,883 
• Modelled Residue Count: 425 
• Deposited Residue Count: 431 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	B [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
QON	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
ZN	E [auth A], F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.184 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.935	α = 90
b = 65.989	β = 90
c = 107.318	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-27 
Deposition Author(s): Talibov, V.O., Eriksson, D.

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Funding Organization	Location	Grant Number
Italian Association for Cancer Research	Italy	IG 19172

Revision History  

• Version 1.0: 2022-07-27
  Type: Initial release
  
• Version 1.1: 2022-09-14
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description