7QNR | pdb_00007qnr

SMYD3 in complex with fragment FL01791

• PDB DOI: https://doi.org/10.2210/pdb7QNR/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-12-22 Released: 2023-04-05 
• Deposition Author(s): Lund, B.A., Cederfelt, D., Dobritzsch, D.
• Funding Organization(s): H2020 Marie Curie Actions of the European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 
  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Identification of fragments targeting SMYD3 using highly sensitive kinetic and multiplexed biosensor-based screening

FitzGerald, E.A., Cederfelt, D., Lund, B.A., Myers, N., Zhang, H., Dobritzsch, D., Danielson, H.

(2024) RSC Med Chem 

• DOI: https://doi.org/10.1039/D4MD00093E

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: homology

Macromolecule Content 

• Total Structure Weight: 50.2 kDa 
• Atom Count: 3,822 
• Modeled Residue Count: 426 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	B [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
E45	F [auth A]	3-propan-2-yl-1,2,4-thiadiazol-5-amine C5 H9 N3 S LSGLMPMOLFSULL-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free:  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.236	α = 90
b = 66.218	β = 90
c = 105.302	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PHENIX	refinement
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-05 
Deposition Author(s): Lund, B.A., Cederfelt, D., Dobritzsch, D.

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Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	European Union	675899

Revision History  

• Version 1.0: 2023-04-05
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description
• Version 1.2: 2024-04-24
  Changes: Database references