Crystal Structure of human RIPK1 kinase domain in complex with a novel inhibitor

Experimental Data Snapshot

  • Resolution: 2.21 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 

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This is version 1.3 of the entry. See complete history


Potent and Selective RIPK1 Inhibitors Targeting Dual-Pockets for the Treatment of Systemic Inflammatory Response Syndrome and Sepsis.

Yang, X.Lu, H.Xie, H.Zhang, B.Nie, T.Fan, C.Yang, T.Xu, Y.Su, H.Tang, W.Zhou, B.

(2022) Angew Chem Int Ed Engl 61: e202114922-e202114922

  • DOI: https://doi.org/10.1002/anie.202114922
  • Primary Citation of Related Structures:  
    7FCZ, 7FD0

  • PubMed Abstract: 

    Sepsis, characterized with high risk of life-threatening organ dysfunction, represents a major cause of health loss and the World Health Organization (WHO) labelled sepsis as the most urgent unmet medical need in 2017. The emerging biological understanding of the role of RIPK1 in sepsis has opened up an exciting opportunity to explore potent and selective RIPK1 inhibitors as an effective therapeutic strategy for SIRS and sepsis therapy. Herein, we have synthesized a class of highly potent dual-mode RIPK1 inhibitors occupying both the allosteric and the ATP binding pockets, exemplified by compound 21 (ZB-R-55) which is about 10-fold more potent than GSK2982772, and exhibits excellent kinase selectivity, good oral pharmacokinetics and good therapeutic effects in the LPS-induced sepsis model, suggesting that compound ZB-R-55 is a highly promising preclinical candidate.

  • Organizational Affiliation

    Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor-interacting serine/threonine-protein kinase 1
A, B
297Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3IF (Subject of Investigation/LOI)
Query on 3IF

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C25 H23 N5 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.21 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.674α = 90
b = 101.705β = 90
c = 129.907γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2022-02-23
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description