4WNM

SYK catalytic domain in complex with a potent triazolopyridine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

A Novel Triazolopyridine-Based Spleen Tyrosine Kinase Inhibitor That Arrests Joint Inflammation.

Ferguson, G.D.Delgado, M.Plantevin-Krenitsky, V.Jensen-Pergakes, K.Bates, R.J.Torres, S.Celeridad, M.Brown, H.Burnett, K.Nadolny, L.Tehrani, L.Packard, G.Pagarigan, B.Haelewyn, J.Nguyen, T.Xu, L.Tang, Y.Hickman, M.Baculi, F.Pierce, S.Miyazawa, K.Jackson, P.Chamberlain, P.LeBrun, L.Xie, W.Bennett, B.Blease, K.

(2016) PLoS One 11: e0145705-e0145705

  • DOI: 10.1371/journal.pone.0145705
  • Primary Citation of Related Structures:  
    4WNM

  • PubMed Abstract: 
  • Autoantibodies and the immunoreceptors to which they bind can contribute to the pathogenesis of autoimmune diseases such as rheumatoid arthritis (RA). Spleen Tyrosine Kinase (Syk) is a non-receptor tyrosine kinase with a central role in immunoreceptor (FcR) signaling and immune cell functionality ...

    Autoantibodies and the immunoreceptors to which they bind can contribute to the pathogenesis of autoimmune diseases such as rheumatoid arthritis (RA). Spleen Tyrosine Kinase (Syk) is a non-receptor tyrosine kinase with a central role in immunoreceptor (FcR) signaling and immune cell functionality. Syk kinase inhibitors have activity in antibody-dependent immune cell activation assays, in preclinical models of arthritis, and have progressed into clinical trials for RA and other autoimmune diseases. Here we describe the characterization of a novel triazolopyridine-based Syk kinase inhibitor, CC-509. This compound is a potent inhibitor of purified Syk enzyme, FcR-dependent and FcR-independent signaling in primary immune cells, and basophil activation in human whole blood. CC-509 is moderately selective across the kinome and against other non-kinase enzymes or receptors. Importantly, CC-509 was optimized away from and has modest activity against cellular KDR and Jak2, kinases that when inhibited in a preclinical and clinical setting may promote hypertension and neutropenia, respectively. In addition, CC-509 is orally bioavailable and displays dose-dependent efficacy in two rodent models of immune-inflammatory disease. In passive cutaneous anaphylaxis (PCA), CC-509 significantly inhibited skin edema. Moreover, CC-509 significantly reduced paw swelling and the tissue levels of pro-inflammatory cytokines RANTES and MIP-1α in the collagen-induced arthritis (CIA) model. In summary, CC-509 is a potent, moderately selective, and efficacious inhibitor of Syk that has a differentiated profile when compared to other Syk compounds that have progressed into the clinic for RA.


    Organizational Affiliation

    Department of Pharmacology, Celgene Corporation, San Diego, California, United States of America.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase SYKA299Homo sapiensMutation(s): 0 
Gene Names: SYK
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P43405 (Homo sapiens)
Explore P43405 
Go to UniProtKB:  P43405
PHAROS:  P43405
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3RT (Subject of Investigation/LOI)
Query on 3RT

Download Ideal Coordinates CCD File 
B [auth A]N~3~-(tetrahydro-2H-pyran-4-yl)-N~6~-[5-(tetrahydro-2H-pyran-4-ylmethyl)[1,2,4]triazolo[1,5-a]pyridin-2-yl]-1H-indazole-3,6-diamine
C24 H29 N7 O2
SHDAHIVOLRESPS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
3RT Binding MOAD:  4WNM Ki: 18 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.871α = 90
b = 84.82β = 90
c = 90.627γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2014-10-13 
  • Released Date: 2016-01-20 
  • Deposition Author(s): Jackson, P.J.

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-20
    Type: Initial release