Structure of human RIPK1 kinase domain in complex with compound 11

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

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Potent and selective inhibitors of receptor-interacting protein kinase 1 that lack an aromatic back pocket group.

Hamilton, G.L.Chen, H.Deshmukh, G.Eigenbrot, C.Fong, R.Johnson, A.Kohli, P.B.Lupardus, P.J.Liederer, B.M.Ramaswamy, S.Wang, H.Wang, J.Xu, Z.Zhu, Y.Vucic, D.Patel, S.

(2019) Bioorg Med Chem Lett 29: 1497-1501

  • DOI: https://doi.org/10.1016/j.bmcl.2019.04.014
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Receptor-interacting protein kinase 1 (RIPK1), a key component of the cellular necroptosis pathway, has gained recognition as an important therapeutic target. Pharmacologic inhibition or genetic inactivation of RIPK1 has shown promise in animal models of disease ranging from acute ischemic conditions, chronic inflammation, and neurodegeneration. We present here a class of RIPK1 inhibitors that is distinguished by a lack of a lipophilic aromatic group present in most literature inhibitors that typically occupies a hydrophobic back pocket of the protein active site. Despite not having this ubiquitous feature of many known RIPK1 inhibitors, we were able to obtain compounds with good potency, kinase selectivity, and pharmacokinetic properties in rats. The use of the lipophilic yet metabolically stable pentafluoroethyl group was critical to balancing the potency and properties of optimized analogs.

  • Organizational Affiliation

    Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor-interacting serine/threonine-protein kinase 1
A, B
310Homo sapiensMutation(s): 0 
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on L4Y

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C19 H22 N4 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
L4Y Binding MOAD:  6NW2 Ki: 16 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.862α = 90
b = 96.644β = 90
c = 125.285γ = 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: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-05-15
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references