5CY3 | pdb_00005cy3

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 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

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 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].
Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
Analytical Sciences & Imaging, Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
Metabolism & Pharmacokinetics, Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA.
Autoimmunity, Transplantation and Inflammation Research, Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.

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 
• Modeled 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.195 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

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