6NYH

Structure of human RIPK1 kinase domain in complex with GNE684


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

RIP1 inhibition blocks inflammatory diseases but not tumor growth or metastases.

Patel, S.Webster, J.D.Varfolomeev, E.Kwon, Y.C.Cheng, J.H.Zhang, J.Dugger, D.L.Wickliffe, K.E.Maltzman, A.Sujatha-Bhaskar, S.Bir Kohli, P.Ramaswamy, S.Deshmukh, G.Liederer, B.M.Fong, R.Hamilton, G.Lupardus, P.Caplazi, P.Lee, W.P.van Lookeren Campagne, M.Johnson, A.McKenzie, B.S.Junttila, M.R.Newton, K.Vucic, D.

(2020) Cell Death Differ. 27: 161-175

  • DOI: 10.1038/s41418-019-0347-0

  • PubMed Abstract: 
  • The kinase RIP1 acts in multiple signaling pathways to regulate inflammatory responses and it can trigger both apoptosis and necroptosis. Its kinase activity has been implicated in a range of inflammatory, neurodegenerative, and oncogenic diseases. H ...

    The kinase RIP1 acts in multiple signaling pathways to regulate inflammatory responses and it can trigger both apoptosis and necroptosis. Its kinase activity has been implicated in a range of inflammatory, neurodegenerative, and oncogenic diseases. Here, we explore the effect of inhibiting RIP1 genetically, using knock-in mice that express catalytically inactive RIP1 D138N, or pharmacologically, using the murine-potent inhibitor GNE684. Inhibition of RIP1 reduced collagen antibody-induced arthritis, and prevented skin inflammation caused by mutation of Sharpin, or colitis caused by deletion of Nemo from intestinal epithelial cells. Conversely, inhibition of RIP1 had no effect on tumor growth or survival in pancreatic tumor models driven by mutant Kras, nor did it reduce lung metastases in a B16 melanoma model. Collectively, our data emphasize a role for the kinase activity of RIP1 in certain inflammatory disease models, but question its relevance to tumor progression and metastases.


    Organizational Affiliation

    Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.,Department of Structural Biology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.,Amgen, South San Francisco, CA, 94080, USA.,Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.,Department of Drug Metabolism and Pharmacokinetics, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.,Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.,Gilead, Foster City, CA, 94404, USA.,Department of Discovery Chemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA. patel.snahel@gene.com.,Department of Translational Immunology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.,Departments of Immunology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.,Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA. domagoj@gene.com.,Department of Molecular Oncology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.,Department of Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.,Department of Discovery Chemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Receptor-interacting serine/threonine-protein kinase 1
A, B
296Homo 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
IOD
Query on IOD

Download SDF File 
Download CCD File 
A, B
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
L8D
Query on L8D

Download SDF File 
Download CCD File 
A, B
(5S)-N-[(3S)-7-methoxy-1-methyl-2-oxo-2,3,4,5-tetrahydro-1H-pyrido[3,4-b]azepin-3-yl]-5-phenyl-6,7-dihydro-5H-pyrrolo[1,2-b][1,2,4]triazole-2-carboxamide
C23 H24 N6 O3
JXFYROJRZJPKTQ-IRXDYDNUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.980α = 90.00
b = 97.034β = 90.00
c = 125.238γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2020-01-01
    Type: Database references