Structure of human RIPK1 kinase domain in complex with GNE684

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

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This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1038/s41418-019-0347-0
  • Primary Citation of Related Structures:  

  • 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. 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 Discovery Chemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA. patel.snahel@gene.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor-interacting serine/threonine-protein kinase 1
A, B
296Homo sapiensMutation(s): 4 
Gene Names: RIPK1RIPRIP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13546 (Homo sapiens)
Explore Q13546 
Go to UniProtKB:  Q13546
PHAROS:  Q13546
GTEx:  ENSG00000137275 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13546
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on L8D

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
C23 H24 N6 O3
Query on IOD

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
H [auth B]
I [auth B]
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.98α = 90
b = 97.034β = 90
c = 125.238γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description