Download MendeleyStructure-based design of potent and selective inhibitors targeting RIPK3 for eliminating on-target toxicity in vitro
Xie, H., Su, H.X., Li, M.J., Xu, Y.C.(2025) Nat Commun
9LFV | pdb_00009lfv
Crystal structure of mouse RIP3 kinase domain complexed with LK01004
- PDB DOI: https://doi.org/10.2210/pdb9LFV/pdb
- Classification: TRANSFERASE
- Organism(s): Mus musculus
- Expression System: Spodoptera frugiperda
- Mutation(s): No
- Deposited: 2025-01-09 Released: 2025-05-07
- Funding Organization(s): Not funded
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.78 ?
- R-Value Free: 0.280 (Depositor), 0.285 (DCC)
- R-Value Work: 0.247 (Depositor), 0.248 (DCC)
- R-Value Observed: 0.249 (Depositor)
Starting Model: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Receptor-interacting serine/threonine-protein kinase 3 | 325 | Mus musculus | Mutation(s): 0 Gene Names: Ripk3, Rip3 EC: 2.7.11.1 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9QZL0 (Mus musculus) Explore Q9QZL0 Go to UniProtKB: Q9QZL0 | |||||
IMPC: MGI:2154952 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9QZL0 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| A1EJP Query on A1EJP | F [auth A], G [auth B], H [auth C], I [auth D] | 3-[2-[(2~{R})-butan-2-yl]-1,3-benzothiazol-5-yl]-1-~{tert}-butyl-pyrazolo[3,4-d]pyrimidin-4-amine C20 H24 N6 S TXNZKZSBYAOTIW-LLVKDONJSA-N |  | ||
| A1EJO Query on A1EJO | E [auth A] | 3-[2-[(2~{S})-butan-2-yl]-1,3-benzothiazol-5-yl]-1-~{tert}-butyl-pyrazolo[3,4-d]pyrimidin-4-amine C20 H24 N6 S TXNZKZSBYAOTIW-NSHDSACASA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.78 ?
- R-Value Free: 0.280 (Depositor), 0.285 (DCC)
- R-Value Work: 0.247 (Depositor), 0.248 (DCC)
- R-Value Observed: 0.249 (Depositor)
Space Group: P 1 21 1
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 56.662 | ¦Á = 90 |
| b = 94.662 | ¦Â = 90.98 |
| c = 122.21 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| Aimless | data scaling |
| PHASER | phasing |
| XDS | data reduction |
Entry History & Funding Information
Deposition Data
| Funding Organization | Location | Grant Number |
|---|---|---|
| Not funded | -- |
Revision History (Full details and data files)
- Version 1.0: 2025-05-07
Type: Initial release
