Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 68.81 kDa 
• Atom Count: 4228 
• Residue Count: 517 
• Unique protein chains: 1

4ITH

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

• DOI: 10.2210/pdb4ITH/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2013-01-18 Released: 2013-03-13 
• Deposition Author(s): Xie, T., Peng, W., Liu, Y., Yan, C., Shi, Y.

---

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 

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

• PubMed: 23473668 
• DOI: 10.1016/j.str.2013.01.016
• Structures With Same Primary Citation


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Receptor-interacting serine/threonine-protein kinase 1	A, B	294	Homo sapiens	Mutation(s): 4  Gene Names: RIPK1, RIP, RIP1 EC: 2.7.11.1
Find proteins for Q13546 (Homo sapiens) Explore Q13546  Go to UniProtKB:  Q13546
NIH Common Fund Data Resources
PHAROS  Q13546 GTEx  ENSG00000137275

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RCM	A, B	(5R)-5-[(7-chloro-1H-indol-3-yl)methyl]-3-methylimidazolidine-2,4-dione C13 H12 Cl N3 O2 WIKGAEMMNQTUGL-SNVBAGLBSA-N
IOD	A, B	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
NA	A, B	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
RCM	IC50 :  316.8999938964844   nM  PDBBind
RCM	IC50:  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 = 47.128	α = 90
b = 93.605	β = 90
c = 129.07	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-01-18 
• Released Date: 2013-03-13 
Deposition Author(s): Xie, T., Peng, W., Liu, Y., Yan, C., Shi, Y.

Revision History 

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