6NYH

Structure of human RIPK1 kinase domain in complex with GNE684

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

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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
  • Primary Citation of Related Structures:  
    6NYH

  • 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 ...

    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. domagoj@gene.com.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor-interacting serine/threonine-protein kinase 1A, B296Homo 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
GTEx:  ENSG00000137275 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13546
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L8D
Query on L8D
Download Ideal Coordinates CCD File 
C [auth A],
G [auth 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
IOD
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]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
L8D Binding MOAD:  6NYH Ki: 21 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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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