4RX8

SYK Catalytic Domain Complexed with a Potent Triazine Inhibitor2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery and profiling of a selective and efficacious syk inhibitor.

Thoma, G.Smith, A.B.van Eis, M.J.Vangrevelinghe, E.Blanz, J.Aichholz, R.Littlewood-Evans, A.Lee, C.C.Liu, H.Zerwes, H.G.

(2015) J.Med.Chem. 58: 1950-1963

  • DOI: 10.1021/jm5018863
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We describe the discovery of selective and potent Syk inhibitor 11, which exhibited favorable PK profiles in rat and dog and was found to be active in a collagen-induced arthritis model in rats. Compound 11 was selected for further profiling, but, un ...

    We describe the discovery of selective and potent Syk inhibitor 11, which exhibited favorable PK profiles in rat and dog and was found to be active in a collagen-induced arthritis model in rats. Compound 11 was selected for further profiling, but, unfortunately, in GLP toxicological studies it showed liver findings in rat and dog. Nevertheless, 11 could become a valuable tool compound to investigate the rich biology of Syk in vitro and in vivo.


    Organizational Affiliation

    Global Discovery Chemistry, ‡Analytical Sciences & Imaging, §Autoimmunity, Transplantation and Inflammation Research, 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
289Homo sapiensMutation(s): 0 
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
3YX
Query on 3YX

Download SDF File 
Download CCD File 
A
3-{[(1R,2S)-2-aminocyclohexyl]amino}-5-(1H-indol-7-ylamino)-1,2,4-triazine-6-carboxamide
C18 H22 N8 O
FPQNRXITKTZFMF-NWDGAFQWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3YXIC50: 23 - 367 nM (99) BINDINGDB
3YXKd: 0.6 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.955α = 90.00
b = 85.333β = 90.00
c = 89.530γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
BUSTER-TNTrefinement
BUSTERrefinement
SCALEPACKdata scaling
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-12-09 
  • Released Date: 2015-03-18 
  • Deposition Author(s): Lee, C.C.

Revision History 

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description