4C8B

Structure of the kinase domain of human RIPK2 in complex with ponatinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Inflammatory Signaling by NOD-RIPK2 Is Inhibited by Clinically Relevant Type II Kinase Inhibitors.

Canning, P.Ruan, Q.Schwerd, T.Hrdinka, M.Maki, J.L.Saleh, D.Suebsuwong, C.Ray, S.Brennan, P.E.Cuny, G.D.Uhlig, H.H.Gyrd-Hansen, M.Degterev, A.Bullock, A.N.

(2015) Chem. Biol. 22: 1174-1184

  • DOI: 10.1016/j.chembiol.2015.07.017

  • PubMed Abstract: 
  • RIPK2 mediates pro-inflammatory signaling from the bacterial sensors NOD1 and NOD2, and is an emerging therapeutic target in autoimmune and inflammatory diseases. We observed that cellular RIPK2 can be potently inhibited by type II inhibitors that di ...

    RIPK2 mediates pro-inflammatory signaling from the bacterial sensors NOD1 and NOD2, and is an emerging therapeutic target in autoimmune and inflammatory diseases. We observed that cellular RIPK2 can be potently inhibited by type II inhibitors that displace the kinase activation segment, whereas ATP-competitive type I inhibition was only poorly effective. The most potent RIPK2 inhibitors were the US Food and Drug Administration-approved drugs ponatinib and regorafenib. Their mechanism of action was independent of NOD2 interaction and involved loss of downstream kinase activation as evidenced by lack of RIPK2 autophosphorylation. Notably, these molecules also blocked RIPK2 ubiquitination and, consequently, inflammatory nuclear factor κB signaling. In monocytes, the inhibitors selectively blocked NOD-dependent tumor necrosis factor production without affecting lipopolysaccharide-dependent pathways. We also determined the first crystal structure of RIPK2 bound to ponatinib, and identified an allosteric site for inhibitor development. These results highlight the potential for type II inhibitors to treat indications of RIPK2 activation as well as inflammation-associated cancers.


    Organizational Affiliation

    Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA.,Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK; Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7LD, UK.,Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX 77204, USA.,Translational Gastroenterology Unit, Nuffield Department of Medicine and Department of Pediatrics, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK.,Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA. Electronic address: alexei.degterev@tufts.edu.,Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK. Electronic address: alex.bullock@sgc.ox.ac.uk.,Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK.,Medical Scientist Training Program and Program in Neuroscience, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA.,Department of Chemistry, University of Houston, Houston, TX 77204, USA.,Center for Neurologic Diseases, Department of Neurology, Brigham & Women's Hospital and Harvard Medical School, Cambridge, MA 02139, USA.,Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RECEPTOR-INTERACTING SERINE/THREONINE-PROTEIN KINASE 2
A, B
334Homo sapiensMutation(s): 0 
Gene Names: RIPK2 (CARDIAK, RICK, RIP2)
EC: 2.7.11.1
Find proteins for O43353 (Homo sapiens)
Go to Gene View: RIPK2
Go to UniProtKB:  O43353
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0LI
Query on 0LI

Download SDF File 
Download CCD File 
A, B
3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzamide
Ponatinib
C29 H27 F3 N6 O
PHXJVRSECIGDHY-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.735α = 90.00
b = 86.682β = 90.00
c = 137.335γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2017-10-25
    Type: Database references