5CY3

SYK catalytic domain complexed with a potent and orally bioavailable benzisothiazole inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5CY3/pdb

• Classification: Transferase/Transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2015-07-30 Released: 2015-09-23 
• Deposition Author(s): Lee, C.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.195 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 

Literature

Orally bioavailable Syk inhibitors with activity in a rat PK/PD model.

Thoma, G., Veenstra, S., Strang, R., Blanz, J., Vangrevelinghe, E., Berghausen, J., Lee, C.C., Zerwes, H.G.

(2015) Bioorg Med Chem Lett 25: 4642-4647

• PubMed: 26320624 
• DOI: https://doi.org/10.1016/j.bmcl.2015.08.037
• Primary Citation of Related Structures:  
  5CXH, 5CXZ, 5CY3


• PubMed Abstract: 
  

  Design and optimization of benzo- and pyrido-thiazoles/isothiazoles are reported leading to the discovery of the potent, orally bioavailable Syk inhibitor 5, which was found to be active in a rat PK/PD model. Compound 5 showed acceptable overall kinase selectivity. However, in addition to Syk it also inhibited Aurora kinase in enzymatic and cellular settings leading to findings in the micronucleus assay. As a consequence, compound 5 was not further pursued.

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Organizational Affiliation: 

Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.2 kDa 
• Atom Count: 2,415 
• Modelled Residue Count: 276 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase SYK	A	291	Homo sapiens	Mutation(s): 1  Gene Names: SYK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P43405 (Homo sapiens) Explore P43405  Go to UniProtKB:  P43405
PHAROS:  P43405 GTEx:  ENSG00000165025

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
55Y	B [auth A]	(5R)-5-[(1R)-1-{[6-(1-methyl-1H-pyrazol-4-yl)-2,1-benzothiazol-4-yl]oxy}ethyl]-1,3-oxazolidin-2-one C16 H16 N4 O3 S MKTGBKHCRFUALQ-RFAUZJTJSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
55Y	BindingDB:  5CY3	IC50: min: 16, max: 737 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.195 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.504	α = 90
b = 37.656	β = 100.14
c = 90.888	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-23 
Deposition Author(s): Lee, C.C.

Revision History  

• Version 1.0: 2015-09-23
  Type: Initial release
  
• Version 1.1: 2015-10-28
  Changes: Database references
• Version 1.2: 2015-12-16
  Changes: Refinement description
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references, Derived calculations