4ITJ

Crystal structure of RIP1 kinase in complex with necrostatin-4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.187 

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:  

  • 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 serie ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Receptor-interacting serine/threonine-protein kinase 1
A, B
294Homo sapiensMutation(s): 4 
Gene Names: RIPK1 (RIP, RIP1)
EC: 2.7.11.1
Find proteins for Q13546 (Homo sapiens)
Go to Gene View: RIPK1
Go to UniProtKB:  Q13546
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A, B
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
1HX
Query on 1HX

Download SDF File 
Download CCD File 
A, B
N-[(1S)-1-(2-chloro-6-fluorophenyl)ethyl]-5-cyano-1-methyl-1H-pyrrole-2-carboxamide
C15 H13 Cl F N3 O
OVRPUVGBRNDNAS-VIFPVBQESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1HXIC50: 377 nM BINDINGMOAD
1HXIC50: 377 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.841α = 90.00
b = 97.136β = 90.00
c = 128.119γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
ADSCdata collection
PHASERphasing
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-13
    Type: Initial release
  • Version 1.1: 2013-03-27
    Type: Database references