3FQS

Crystal structure of spleen tyrosine kinase complexed with R406


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights for design of potent spleen tyrosine kinase inhibitors from crystallographic analysis of three inhibitor complexes.

Villasenor, A.G.Kondru, R.Ho, H.Wang, S.Papp, E.Shaw, D.Barnett, J.W.Browner, M.F.Kuglstatter, A.

(2009) Chem Biol Drug Des 73: 466-470

  • DOI: 10.1111/j.1747-0285.2009.00785.x
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Spleen tyrosine kinase is considered an attractive drug target for the treatment of allergic and antibody mediated autoimmune diseases. We have determined the co-crystal structures of spleen tyrosine kinase complexed with three known inhibitors: YM19 ...

    Spleen tyrosine kinase is considered an attractive drug target for the treatment of allergic and antibody mediated autoimmune diseases. We have determined the co-crystal structures of spleen tyrosine kinase complexed with three known inhibitors: YM193306, a 7-azaindole derivative and R406. The cis-cyclohexyldiamino moiety of YM193306 is forming four hydrophobically shielded polar interactions with the spleen tyrosine kinase protein and is therefore crucial for the high potency of this inhibitor. Its primary amino group is inducing a conformational change of the spleen tyrosine kinase DFG Asp side chain. The crystal structure of the 7-azaindole derivative bound to spleen tyrosine kinase is the first demonstration of a 2-substituted 7-azaindole bound to a protein kinase. Its indole-amide substituent is tightly packed between the N- and C-terminal kinase lobes. The co-crystal structure of the spleen tyrosine kinase-R406 complex shows two main differences to the previously reported structure of spleen tyrosine kinase soaked with R406: (i) the side chain of the highly conserved Lys is disordered and not forming a hydrogen bond to R406 and (ii) the DFG Asp side chain is pointing away from and not towards R406. The novel protein-ligand interactions and protein conformational changes revealed in these structures guide the rational design and structure-based optimization of second-generation spleen tyrosine kinase inhibitors.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Chicago, Center for Integrative Science, Chicago, Illinois, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase SYK
A
291Homo sapiensMutation(s): 0 
Gene Names: SYK
EC: 2.7.10.2
Find proteins for P43405 (Homo sapiens)
Go to UniProtKB:  P43405
NIH Common Fund Data Resources
PHAROS  P43405
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
585
Query on 585

Download CCD File 
A
6-({5-fluoro-2-[(3,4,5-trimethoxyphenyl)amino]pyrimidin-4-yl}amino)-2,2-dimethyl-2H-pyrido[3,2-b][1,4]oxazin-3(4H)-one
C22 H23 F N6 O5
NHHQJBCNYHBUSI-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
585IC50:  3354   nM  BindingDB
585EC50:  48   nM  BindingDB
585EC50:  56   nM  BindingDB
585EC50:  53   nM  BindingDB
585EC50:  3659   nM  BindingDB
585IC50:  41   nM  BindingDB
585EC50:  335   nM  BindingDB
585IC50:  457   nM  BindingDB
585Ki:  30   nM  BindingDB
585IC50:  5.5   nM  BindingDB
585EC50:  111   nM  BindingDB
585IC50 :  41   nM  PDBBind
585IC50:  68   nM  BindingDB
585IC50:  41   nM  Binding MOAD
585EC50:  33   nM  BindingDB
585EC50:  10   nM  BindingDB
585EC50:  151   nM  BindingDB
585IC50:  64   nM  BindingDB
585Kd:  19   nM  BindingDB
585EC50:  171   nM  BindingDB
585IC50:  23.6200008392334   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.971α = 90
b = 85.079β = 90
c = 91.144γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection, Refinement description