5LMB

HUMAN SPLEEN TYROSINE KINASE KINASE DOMAIN IN COMPLEX WITH AZANAPHTHYRIDINE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Optimisation of a novel series of potent and orally bioavailable azanaphthyridine SYK inhibitors.

Garton, N.S.Barker, M.D.Davis, R.P.Douault, C.Hooper-Greenhill, E.Jones, E.Lewis, H.D.Liddle, J.Lugo, D.McCleary, S.Preston, A.G.Ramirez-Molina, C.Neu, M.Shipley, T.J.Somers, D.O.Watson, R.J.Wilson, D.M.

(2016) Bioorg.Med.Chem.Lett. 26: 4606-4612

  • DOI: 10.1016/j.bmcl.2016.08.070
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The optimisation of the azanaphthyridine series of Spleen Tyrosine Kinase inhibitors is described. The medicinal chemistry strategy was focused on optimising the human whole blood activity whilst achieving a sufficient margin over hERG activity. A go ...

    The optimisation of the azanaphthyridine series of Spleen Tyrosine Kinase inhibitors is described. The medicinal chemistry strategy was focused on optimising the human whole blood activity whilst achieving a sufficient margin over hERG activity. A good pharmacokinetic profile was achieved by modification of the pKa. Morpholine compound 32 is a potent SYK inhibitor showing moderate selectivity, good oral bioavailability and good efficacy in the rat Arthus model but demonstrated a genotoxic potential in the Ames assay.


    Organizational Affiliation

    GlaxoSmithKline R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK. Electronic address: Neil.S.Garton@gsk.com.,GlaxoSmithKline R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK.,AstraZeneca, Hodgkin Building, Chesterford Research Campus, Little Chesterford, Saffron Walden, Cambs. CB10 1XL, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase SYK
A, B
277Homo 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, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
6ZF
Query on 6ZF

Download SDF File 
Download CCD File 
A, B
7-[6-(dimethylamino)pyridin-3-yl]-~{N}-[[(3~{S})-piperidin-3-yl]methyl]pyrido[3,4-b]pyrazin-5-amine
C20 H25 N7
CLKZDZYGBHNPSM-AWEZNQCLSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A, B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6ZFIC50: 16 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.175 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 39.849α = 99.81
b = 41.780β = 90.41
c = 86.991γ = 100.03
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-07-29 
  • Released Date: 2016-09-14 
  • Deposition Author(s): Somers, D.O., Neu, M.

Revision History 

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2016-09-21
    Type: Database references
  • Version 1.2: 2019-04-03
    Type: Data collection, Source and taxonomy