6OCQ

Crystal structure of RIP1 kinase in complex with a pyrrolidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.793 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery and Lead-Optimization of 4,5-Dihydropyrazoles as Mono-Kinase Selective, Orally Bioavailable and Efficacious Inhibitors of Receptor Interacting Protein 1 (RIP1) Kinase.

Harris, P.A.Faucher, N.George, N.Eidam, P.M.King, B.W.White, G.V.Anderson, N.A.Bandyopadhyay, D.Beal, A.M.Beneton, V.Berger, S.B.Campobasso, N.Campos, S.Capriotti, C.A.Cox, J.A.Daugan, A.Donche, F.Fouchet, M.H.Finger, J.N.Geddes, B.Gough, P.J.Grondin, P.Hoffman, B.L.Hoffman, S.J.Hutchinson, S.E.Jeong, J.U.Jigorel, E.Lamoureux, P.Leister, L.K.Lich, J.D.Mahajan, M.K.Meslamani, J.Mosley, J.E.Nagilla, R.Nassau, P.M.Ng, S.L.Ouellette, M.T.Pasikanti, K.K.Potvain, F.Reilly, M.A.Rivera, E.J.Sautet, S.Schaeffer, M.C.Sehon, C.A.Sun, H.Thorpe, J.H.Totoritis, R.D.Ward, P.Wellaway, N.Wisnoski, D.D.Woolven, J.M.Bertin, J.Marquis, R.W.

(2019) J.Med.Chem. 62: 5096-5110

  • DOI: 10.1021/acs.jmedchem.9b00318
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • RIP1 kinase regulates necroptosis and inflammation and may play an important role in contributing to a variety of human pathologies, including inflammatory and neurological diseases. Currently, RIP1 kinase inhibitors have advanced into early clinical ...

    RIP1 kinase regulates necroptosis and inflammation and may play an important role in contributing to a variety of human pathologies, including inflammatory and neurological diseases. Currently, RIP1 kinase inhibitors have advanced into early clinical trials for evaluation in inflammatory diseases such as psoriasis, rheumatoid arthritis, and ulcerative colitis and neurological diseases such as amyotrophic lateral sclerosis and Alzheimer's disease. In this paper, we report on the design of potent and highly selective dihydropyrazole (DHP) RIP1 kinase inhibitors starting from a high-throughput screen and the lead-optimization of this series from a lead with minimal rat oral exposure to the identification of dihydropyrazole 77 with good pharmacokinetic profiles in multiple species. Additionally, we identified a potent murine RIP1 kinase inhibitor 76 as a valuable in vivo tool molecule suitable for evaluating the role of RIP1 kinase in chronic models of disease. DHP 76 showed efficacy in mouse models of both multiple sclerosis and human retinitis pigmentosa.


    Organizational Affiliation

    Flexible Discovery Unit , GlaxoSmithKline , 25-27 avenue du Qu├ębec , 91951 Les Ulis Cedex , France.,Flexible Discovery Unit , GlaxoSmithKline , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Receptor-interacting serine/threonine-protein kinase 1
A, B
303Homo sapiensMutation(s): 4 
Gene Names: RIPK1 (RIP, RIP1)
EC: 2.7.11.1
Find proteins for Q13546 (Homo sapiens)
Go to Gene View: RIPK1
Go to UniProtKB:  Q13546
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
M5J
Query on M5J

Download SDF File 
Download CCD File 
A, B
1-[(2S)-2-(3-fluorophenyl)pyrrolidin-1-yl]-2,2-dimethylpropan-1-one
C15 H20 F N O
KAKAXRVKJWUSTC-ZDUSSCGKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.793 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.297α = 90.00
b = 95.117β = 90.00
c = 127.240γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-06-05
    Type: Data collection, Database references