6R5F

Crystal structure of RIP1 kinase in complex with DHP77

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 

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Ligand Structure Quality Assessment 


This is version 1.2 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:  
    6OCQ, 6R5F

  • 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 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 ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor-interacting serine/threonine-protein kinase 1A, B, C, D303Homo sapiensMutation(s): 4 
Gene Names: RIPK1, RIP, RIP1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13546 (Homo sapiens)
Explore Q13546 
Go to UniProtKB:  Q13546
PHAROS:  Q13546
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13546
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JSW (Subject of Investigation/LOI)
Query on JSW
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
H [auth D]		[(5~{S})-5-[3,5-bis(fluoranyl)phenyl]pyrazolidin-1-yl]-[1-(5-methyl-1,3,4-oxadiazol-2-yl)piperidin-4-yl]methanone
C18 H21 F2 N5 O2
KYFXWICBRBBWQQ-INIZCTEOSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.858α = 90
b = 138.919β = 96.5
c = 96.534γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
AutoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-06-05
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-21
    Changes: Data collection