9GTG | pdb_00009gtg

RIPK1 in complex with AZ"902


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.295 (Depositor), 0.293 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.221 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery and Validation of a Novel Class of Necroptosis Inhibitors Targeting RIPK1.

Soday, L.Seripracharat, C.Gray, J.L.Luz, A.F.S.Howard, R.T.Singh, R.Burden, T.J.Bernardini, E.Mateus-Pinheiro, M.Petersen, J.Gunnarsson, A.Gunnarsson, J.Aagaard, A.Sjogren, T.Maslen, S.Bartlett, E.J.Iles, A.F.Smith, D.M.Scott, J.S.Skehel, M.Davis, A.M.Ressurreicao, A.S.Moreira, R.Rodrigues, C.M.P.Shenoy, A.R.Tate, E.W.

(2025) ACS Chem Biol 20: 1527-1543

  • DOI: https://doi.org/10.1021/acschembio.5c00112
  • Primary Citation Related Structures: 
    9GTG, 9GTY

  • PubMed Abstract: 

    Necroptosis is a form of programmed cell death that, when dysregulated, is associated with cancer and inflammatory and neurodegenerative diseases. Here, starting from hits identified from a phenotypic high-throughput screen for inhibitors of necroptosis, we synthesized a library of compounds containing a 7-phenylquinoline motif and validated their anti-necroptotic activity in a novel live-cell assay. Based on these data, we designed an optimized photoaffinity probe for target engagement studies and through biochemical and cell-based assays established receptor-interacting kinase 1 (RIPK1) as the cellular target, with inhibition of necroptosis arising from the prevention of RIPK1 autophosphorylation and activation. X-ray crystallography and mass spectrometry revealed that these compounds bind at the hinge region of the active conformation of RIPK1, establishing them as type I kinase inhibitors. In addition, we demonstrated in vitro synergy with type III kinase inhibitors, such as necrostatin-1 and found that lead compounds protected mice against acute inflammation in necroptosis models in vivo . Overall, we present a novel pharmacophore for inhibition of human RIPK1, a key protein involved in necroptosis, and provide a photoaffinity probe to explore RIPK1 target engagement in cells.


  • Organizational Affiliation
    • Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.

Macromolecule Content 

  • Total Structure Weight: 72.59 kDa 
  • Atom Count: 4,225 
  • Modeled Residue Count: 518 
  • Deposited Residue Count: 626 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Receptor-interacting serine/threonine-protein kinase 1
A, B
313Homo sapiensMutation(s): 0 
Gene Names: RIPK1RIPRIP1
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
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.295 (Depositor), 0.293 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.084α = 90
b = 96.491β = 90
c = 129.002γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2025-07-02 
  • Deposition Author(s): Petersen, J.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Source and taxonomy
  • Version 1.2: 2025-07-30
    Changes: Database references