Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 139.90 kDa 
• Atom Count: 8230 
• Modelled Residue Count: 1011 
• Deposited Residue Count: 1212 
• Unique protein chains: 1

6R5F

Crystal structure of RIP1 kinase in complex with DHP77

• DOI: 10.2210/pdb6R5F/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Baculovirus expression vector pFastBac1-HM
• Mutation(s): Yes 


• Deposited: 2019-03-25 Released: 2019-05-01 
• Deposition Author(s): Thorpe, J.H., Campobasso, N., Harris, P.A.

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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 

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

• PubMed: 31013427 
• 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. 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.

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Organizational Affiliation: 

Flexible Discovery Unit , GlaxoSmithKline , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-interacting serine/threonine-protein kinase 1	A, B, C, D	303	Homo sapiens	Mutation(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 GTEx:  ENSG00000137275

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JSW (Subject of Investigation/LOI)	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

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 = 45.858	α = 90
b = 138.919	β = 96.5
c = 96.534	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
AutoPROC	data scaling
PHASER	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2019-03-25 
• Released Date: 2019-05-01 
Deposition Author(s): Thorpe, J.H., Campobasso, N., Harris, P.A.

Revision History  

• 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