9IWY | pdb_00009iwy

Crystal structure of the mouse RIP3 kinase domain in complexed with LK01003

PDB DOI: https://doi.org/10.2210/pdb9IWY/pdb

Classification: TRANSFERASE
Organism(s): Mus musculus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-07-26 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: 2.52 ?
R-Value Free:
0.299 (Depositor), 0.295 (DCC)
R-Value Work:
0.269 (Depositor), 0.270 (DCC)
R-Value Observed:
0.270 (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

Structure-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

Macromolecule Content

Total Structure Weight: 73.33 kDa
Atom Count: 3,778
Modelled Residue Count: 492
Deposited Residue Count: 650
Unique protein chains: 1

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	A, B	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 Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1D97 (Subject of Investigation/LOI) Query on A1D97 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	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		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.52 ?
R-Value Free: 0.299 (Depositor), 0.295 (DCC)
R-Value Work: 0.269 (Depositor), 0.270 (DCC)
R-Value Observed: 0.270 (Depositor)

Space Group: P 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 47.7	α = 99.26
b = 56.157	β = 114.15
c = 57.975	γ = 89.91

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
xia2	data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-05-07
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.