4PX6

SYK catalytic domain in complex with a potent pyridopyrimidinone inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Syk inhibitors with high potency in presence of blood.

Thoma, G.Blanz, J.Buhlmayer, P.Druckes, P.Kittelmann, M.Smith, A.B.van Eis, M.Vangrevelinghe, E.Zerwes, H.G.Che, J.J.He, X.Jin, Y.Lee, C.C.Michellys, P.Y.Uno, T.Liu, H.

(2014) Bioorg.Med.Chem.Lett. 24: 2278-2282

  • DOI: 10.1016/j.bmcl.2014.03.075

  • PubMed Abstract: 
  • We describe two series of Syk inhibitors which potently abrogate Syk kinase function in enzymatic assays, cellular assays and in primary cells in the presence of blood. Introduction of a 7-aminoindole substituent led to derivatives with good kinase s ...

    We describe two series of Syk inhibitors which potently abrogate Syk kinase function in enzymatic assays, cellular assays and in primary cells in the presence of blood. Introduction of a 7-aminoindole substituent led to derivatives with good kinase selectivity and little or no hERG channel inhibition (3b, 10c).


    Organizational Affiliation

    Novartis Institutes for Biomedical Research, Forum 1 Novartis Campus, 4056 Basel, Switzerland. Electronic address: gebhard.thoma@novartis.com.




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
2X6
Query on 2X6

Download SDF File 
Download CCD File 
A
7-{[(1R,2S)-2-aminocyclohexyl]amino}-5-(1H-indol-7-ylamino)pyrido[4,3-d]pyrimidin-4(3H)-one
C21 H23 N7 O
JZLUCFJMWJDRIK-UONOGXRCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2X6IC50: 4 - 307 nM (99) BINDINGDB
2X6IC50: 4 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.889α = 90.00
b = 85.161β = 90.00
c = 88.961γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
REFMACrefinement
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-03-21 
  • Released Date: 2014-04-23 
  • Deposition Author(s): Lee, C.C.

Revision History 

  • Version 1.0: 2014-04-23
    Type: Initial release
  • Version 1.1: 2014-05-21
    Type: Database references