9LFU | pdb_00009lfu

Crystal structure of human RIP3 kinase domain complexed with LK01003

• PDB DOI: https://doi.org/10.2210/pdb9LFU/pdb

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


• Deposited: 2025-01-09 Released: 2025-05-07 
• Deposition Author(s): Xie, H., Su, H.X., Li, M.J., Xu, Y.C.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.93 Å
• R-Value Free: 
  0.319 (Depositor), 0.307 (DCC) 
• R-Value Work: 
  0.258 (Depositor) 
• R-Value Observed: 
  0.261 (Depositor) 

Starting Model: experimental

Literature

Structure-based design of potent and selective inhibitors targeting RIPK3 for eliminating on-target toxicity in vitro.

Su, H., Chen, G., Xie, H., Li, W., Xiong, M., He, J., Hu, H., Zhao, W., Shao, Q., Li, M., Zhao, Q., Xu, Y.

(2025) Nat Commun 16: 4288-4288

• PubMed: 40341069 
• DOI: https://doi.org/10.1038/s41467-025-59432-8
• Primary Citation Related Structures: 
  9IWW, 9IWX, 9IWY, 9IWZ, 9IX0, 9IX1, 9IX2, 9IX3, 9LFU, 9LFV, 9LFW


• PubMed Abstract: 
  

  The essential role of RIPK3 in necroptosis makes its inhibition a promising therapeutic strategy. However, the development of RIPK3 inhibitors has been hampered by on-target apoptosis and limited kinase selectivity. Inspired by the R69H mutation, which prevents on-target apoptosis by disrupting RIPK3 dimerization, we design LK-series inhibitors that effectively inhibit RIPK3 in biochemical assays and block TNF-α-induced necroptosis in both mouse L929 and human HT29 cells without inducing apoptosis. The representative compound, LK01003, shows high selectivity across a panel of 379 kinases. Our structural studies reveal that LK compounds act as Type I ^1/2 inhibitors, engaging a unique hydrophobic site and stabilizing an inactive conformation of RIPK3. Moreover, several type II inhibitors are also revealed to maintain RIPK3 in the inactive conformation and do not induce on-target apoptosis. These findings suggest a promising strategy for rational design of safe and selective inhibitors by locking the inactive conformation of RIPK3.

---

Organizational Affiliation: 
• State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, 201203, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, 100049, China. [e-mail].
School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, University of Nottingham Ningbo China, Ningbo, 315100, China.
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, 201203, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China.
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, 201203, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, 100049, China. [e-mail].
School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China. [e-mail].
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, 201203, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, 100049, China. [e-mail].
School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 78.14 kDa 
• Atom Count: 4,540 
• Modeled Residue Count: 570 
• Deposited Residue Count: 692 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-interacting serine/threonine-protein kinase 3	A, B	346	Homo sapiens	Mutation(s): 2  Gene Names: RIPK3, RIP3 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y572 (Homo sapiens) Explore Q9Y572  Go to UniProtKB:  Q9Y572
PHAROS:  Q9Y572 GTEx:  ENSG00000129465

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D97	C [auth A], D [auth B]	2-cyclopentyl-~{N}-(6-propan-2-ylsulfonylquinolin-4-yl)-1,3-benzothiazol-5-amine C24 H25 N3 O2 S2 PVKIFNZMYGMWPD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.93 Å
• R-Value Free:  0.319 (Depositor), 0.307 (DCC) 
• R-Value Work:  0.258 (Depositor) 
• R-Value Observed: 0.261 (Depositor) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.203	α = 90
b = 129.203	β = 90
c = 79.429	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-05-07 
Deposition Author(s): Xie, H., Su, H.X., Li, M.J., Xu, Y.C.

---

Funding Organization	Location	Grant Number
Not funded	China	--

Revision History  

• Version 1.0: 2025-05-07
  Type: Initial release
  
• Version 1.1: 2025-05-21
  Changes: Database references