4YND | pdb_00004ynd

The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2

• PDB DOI: https://doi.org/10.2210/pdb4YND/pdb

• Classification: Transferase/Inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2015-03-09 Released: 2015-05-20 
• Deposition Author(s): Sweis, R.F., Wang, Z., Algire, M., Arrowsmith, C.H., Brown, P.J., Chiang, G.C., Guo, J., Jakob, C.G., Kennedy, S., Li, F., Soni, N.B., Vedadi, M., Pappano, W.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 
  0.253 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.198 (Depositor) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2.

Sweis, R.F., Wang, Z., Algire, M., Arrowsmith, C.H., Brown, P.J., Chiang, G.G., Guo, J., Jakob, C.G., Kennedy, S., Li, F., Maag, D., Shaw, B., Soni, N.B., Vedadi, M., Pappano, W.N.

(2015) ACS Med Chem Lett 6: 695-700

• PubMed: 26101576 
• DOI: https://doi.org/10.1021/acsmedchemlett.5b00124
• Primary Citation Related Structures: 
  4YND


• PubMed Abstract: 
  

  A lack of useful small molecule tools has precluded thorough interrogation of the biological function of SMYD2, a lysine methyltransferase with known tumor-suppressor substrates. Systematic exploration of the structure-activity relationships of a previously known benzoxazinone compound led to the synthesis of A-893, a potent and selective SMYD2 inhibitor (IC50: 2.8 nM). A cocrystal structure reveals the origin of enhanced potency, and effective suppression of p53K370 methylation is observed in a lung carcinoma (A549) cell line.

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Organizational Affiliation: 
• Discovery Research, AbbVie, Inc. , 1 North Waukegan Road, North Chicago, Illinois 60064, United States.
Structural Genomics Consortium, University of Toronto , Toronto, ON M5G 1L7, Canada ; Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto , Toronto, ON M5G 2M9, Canada.
Structural Genomics Consortium, University of Toronto , Toronto, ON M5G 1L7, Canada.
Structural Genomics Consortium, University of Toronto , Toronto, ON M5G 1L7, Canada ; Department of Pharmacology and Toxicology, University of Toronto , Toronto, ON M5S 1A8, Canada.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 54.38 kDa 
• Atom Count: 3,633 
• Modeled Residue Count: 428 
• Deposited Residue Count: 461 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-lysine methyltransferase SMYD2	A	461	Homo sapiens	Mutation(s): 0  Gene Names: SMYD2, KMT3C EC: 2.1.1 (PDB Primary Data), 2.1.1.43 (PDB Primary Data), 2.1.1.354 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRG4 (Homo sapiens) Explore Q9NRG4  Go to UniProtKB:  Q9NRG4
PHAROS:  Q9NRG4 GTEx:  ENSG00000143499

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4GQ	E [auth A]	N-cyclohexyl-N~3~-[2-(3,4-dichlorophenyl)ethyl]-N-(2-{[(2R)-2-hydroxy-2-(3-oxo-3,4-dihydro-2H-1,4-benzoxazin-8-yl)ethyl]amino}ethyl)-beta-alaninamide C29 H38 Cl2 N4 O4 WVRBXBROEPXZHF-SANMLTNESA-N
SAM	F [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4GQ	BindingDB:  4YND	IC50: min: 2.8, max: 23 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free:  0.253 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.198 (Depositor) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.796	α = 90
b = 71.301	β = 90
c = 118.93	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-20 
Deposition Author(s): Sweis, R.F., Wang, Z., Algire, M., Arrowsmith, C.H., Brown, P.J., Chiang, G.C., Guo, J., Jakob, C.G., Kennedy, S., Li, F., Soni, N.B., Vedadi, M., Pappano, W.N.

Revision History  

• Version 1.0: 2015-05-20
  Type: Initial release
  
• Version 1.1: 2015-07-08
  Changes: Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary