6HMX

RIP2 Kinase Catalytic Domain complex with N(4,5dimethyl1Hpyrazol3yl)7methoxy6(2methylpropane2sulfonyl)quinolin4amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Identification of Quinoline-Based RIP2 Kinase Inhibitors with an Improved Therapeutic Index to the hERG Ion Channel.

Haile, P.A.Casillas, L.N.Bury, M.J.Mehlmann, J.F.Singhaus Jr., R.Charnley, A.K.Hughes, T.V.DeMartino, M.P.Wang, G.Z.Romano, J.J.Dong, X.Plotnikov, N.V.Lakdawala, A.S.Convery, M.A.Votta, B.J.Lipshutz, D.B.Desai, B.M.Swift, B.Capriotti, C.A.Berger, S.B.Mahajan, M.K.Reilly, M.A.Rivera, E.J.Sun, H.H.Nagilla, R.LePage, C.Ouellette, M.T.Totoritis, R.D.Donovan, B.T.Brown, B.S.Chaudhary, K.W.Gough, P.J.Bertin, J.Marquis, R.W.

(2018) ACS Med Chem Lett 9: 1039-1044

  • DOI: 10.1021/acsmedchemlett.8b00344
  • Primary Citation of Related Structures:  
    6HMX

  • PubMed Abstract: 
  • RIP2 kinase was recently identified as a therapeutic target for a variety of autoimmune diseases. We have reported previously a selective 4-aminoquinoline-based RIP2 inhibitor GSK583 and demonstrated its effectiveness in blocking downstream NOD2 signaling in cellular models, rodent in vivo models, and human ex vivo disease models ...

    RIP2 kinase was recently identified as a therapeutic target for a variety of autoimmune diseases. We have reported previously a selective 4-aminoquinoline-based RIP2 inhibitor GSK583 and demonstrated its effectiveness in blocking downstream NOD2 signaling in cellular models, rodent in vivo models, and human ex vivo disease models. While this tool compound was valuable in validating the biological pathway, it suffered from activity at the hERG ion channel and a poor PK/PD profile thereby limiting progression of this analog. Herein, we detail our efforts to improve both this off-target liability as well as the PK/PD profile of this series of inhibitors through modulation of lipophilicity and strengthening hinge binding ability. These efforts have led to inhibitor 7 , which possesses high binding affinity for the ATP pocket of RIP2 (IC 50 = 1 nM) and inhibition of downstream cytokine production in human whole blood (IC 50 = 10 nM) with reduced hERG activity (14 μM).


    Organizational Affiliation

    GlaxoSmithKline, Collegeville Road, Collegeville, Pennsylvania 19426, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor-interacting serine/threonine-protein kinase 2A, B311Homo sapiensMutation(s): 0 
Gene Names: RIPK2CARDIAKRICKRIP2UNQ277/PRO314/PRO34092
EC: 2.7.11.1 (PDB Primary Data), 2.7.10.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O43353 (Homo sapiens)
Explore O43353 
Go to UniProtKB:  O43353
PHAROS:  O43353
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GEZ (Subject of Investigation/LOI)
Query on GEZ

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]6-~{tert}-butylsulfonyl-~{N}-(3,4-dimethyl-1~{H}-pyrazol-5-yl)-7-methoxy-quinolin-4-amine
C19 H24 N4 O3 S
LHPFRDAGGDMRMZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.541α = 90
b = 132.541β = 90
c = 107.179γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release