6OCQ

Crystal structure of RIP1 kinase in complex with a pyrrolidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

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:  
    6R5F, 6OCQ

  • 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 , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor-interacting serine/threonine-protein kinase 1AB303Homo sapiensMutation(s): 4 
Gene Names: RIPK1RIPRIP1
EC: 2.7.11.1
Find proteins for Q13546 (Homo sapiens)
Explore Q13546 
Go to UniProtKB:  Q13546
NIH Common Fund Data Resources
PHAROS  Q13546
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M5J
Query on M5J

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
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.297α = 90
b = 95.117β = 90
c = 127.24γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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