4ITH

Crystal structure of RIP1 kinase in complex with necrostatin-1 analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural Basis of RIP1 Inhibition by Necrostatins.

Xie, T.Peng, W.Liu, Y.Yan, C.Maki, J.Degterev, A.Yuan, J.Shi, Y.

(2013) Structure 21: 493-499

  • DOI: https://doi.org/10.1016/j.str.2013.01.016
  • Primary Citation of Related Structures:  
    4ITH, 4ITI, 4ITJ

  • PubMed Abstract: 

    Necroptosis is a cellular mechanism that mediates necrotic cell death. The receptor-interacting serine/threonine protein kinase 1 (RIP1) is an essential upstream signaling molecule in tumor-necrosis-factor-α-induced necroptosis. Necrostatins, a series of small-molecule inhibitors, suppress necroptosis by specifically inhibiting RIP1 kinase activity. Both RIP1 structure and the mechanisms by which necrostatins inhibit RIP1 remain unknown. Here, we report the crystal structures of the RIP1 kinase domain individually bound to necrostatin-1 analog, necrostatin-3 analog, and necrostatin-4. Necrostatin, caged in a hydrophobic pocket between the N- and C-lobes of the kinase domain, stabilizes RIP1 in an inactive conformation through interactions with highly conserved amino acids in the activation loop and the surrounding structural elements. Structural comparison of RIP1 with the inhibitor-bound oncogenic kinase B-RAF reveals partially overlapping binding sites for necrostatin and for the anticancer compound PLX4032. Our study provides a structural basis for RIP1 inhibition by necrostatins and offers insights into potential structure-based drug design.


  • Organizational Affiliation

    Ministry of Education Protein Science Laboratory, State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor-interacting serine/threonine-protein kinase 1
A, B
294Homo sapiensMutation(s): 4 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RCM
Query on RCM

Download Ideal Coordinates CCD File 
I [auth A],
P [auth B]
(5R)-5-[(7-chloro-1H-indol-3-yl)methyl]-3-methylimidazolidine-2,4-dione
C13 H12 Cl N3 O2
WIKGAEMMNQTUGL-SNVBAGLBSA-N
IOD
Query on IOD

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth A],
O [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
RCM PDBBind:  4ITH IC50: 316.9 (nM) from 1 assay(s)
BindingDB:  4ITH IC50: min: 200, max: 630 (nM) from 3 assay(s)
EC50: 18 (nM) from 1 assay(s)
Binding MOAD:  4ITH IC50: 316.9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.128α = 90
b = 93.605β = 90
c = 129.07γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data 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: 2013-03-13
    Type: Initial release
  • Version 1.1: 2013-03-27
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description