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 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor-interacting serine/threonine-protein kinase 1A, B294Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / 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		 Ligand Interaction
IOD
Query on IOD
Download Ideal Coordinates CCD File 
C [auth A] , D [auth A] , E [auth A] , F [auth A] , G [auth A] , J [auth B] , K [auth B] , L [auth B] , 
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		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
 H [auth A], O [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RCMIC50:  320   nM  BindingDB
RCMIC50:  630   nM  BindingDB
RCMIC50 :  316.8999938964844   nM  PDBBind
RCMIC50:  200   nM  BindingDB
RCMEC50:  18   nM  BindingDB
RCMIC50:  316.9000244140625   nM  Binding MOAD
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

View Full Validation Report


View more in-depth experimental data

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