5CY3

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1016/j.bmcl.2015.08.037
  • Primary Citation of Related Structures:  

  • 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 kina ...

    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.


    Organizational Affiliation

    Analytical Sciences & Imaging, Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.,Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland. Electronic address: gebhard.thoma@novartis.com.,Autoimmunity, Transplantation and Inflammation Research, 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.,Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase SYK
A
291Homo sapiensMutation(s): 1 
Gene Names: SYK
EC: 2.7.10.2
Find proteins for P43405 (Homo sapiens)
Go to Gene View: SYK
Go to UniProtKB:  P43405
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
55Y
Query on 55Y

Download SDF File 
Download CCD File 
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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
55YIC50: 16 - 737 nM (99) BINDINGDB
55YIC50: 16 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.504α = 90.00
b = 37.656β = 100.14
c = 90.888γ = 90.00
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
REFMACphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-07-30 
  • 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
    Type: Database references
  • Version 1.2: 2015-12-16
    Type: Refinement description