6S1F

Structure of the kinase domain of human RIPK2 in complex with the inhibitor CSLP3

• PDB DOI: https://doi.org/10.2210/pdb6S1F/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2019-06-18 Released: 2019-10-16 
• Deposition Author(s): Pinkas, D.M., Bufton, J.C., Kupinska, K., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.N.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.11 Å
• R-Value Free: 0.300 
• R-Value Work: 0.254 
• R-Value Observed: 0.256 

Starting Model: experimental

Literature

Design of 3,5-diaryl-2-aminopyridines as receptor-interacting protein kinase 2 (RIPK2) and nucleotide-binding oligomerization domain (NOD) cell signaling inhibitors

Suebsuwong, C., Dai, B., Pinkas, D.M., Bufton, J.C., Duddupudi, A.L., Li, L., Hrdinka, M., Schlicher, L., Gyrd-Hansen, M., Hu, M., Bullock, A.N., Degterev, A., Cuny, G.D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 147.36 kDa 
• Atom Count: 9,422 
• Modelled Residue Count: 1,154 
• Deposited Residue Count: 1,268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-interacting serine/threonine-protein kinase 2	A, B, C, D	317	Homo sapiens	Mutation(s): 0  Gene Names: RIPK2, CARDIAK, RICK, RIP2, UNQ277/PRO314/PRO34092 EC: 2.7.11.1 (PDB Primary Data), 2.7.10.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O43353 (Homo sapiens) Explore O43353  Go to UniProtKB:  O43353
PHAROS:  O43353 GTEx:  ENSG00000104312

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KRE (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	~{N}-[3-[2-azanyl-5-(4-piperazin-1-ylphenyl)pyridin-3-yl]-5-methoxy-phenyl]methanesulfonamide C23 H27 N5 O3 S WTNLXMJMLHJDKF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
KRE	BindingDB:  6S1F	IC50: 51 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.11 Å
• R-Value Free: 0.300 
• R-Value Work: 0.254 
• R-Value Observed: 0.256 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.343	α = 90
b = 124.343	β = 90
c = 228.676	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-10-16 
Deposition Author(s): Pinkas, D.M., Bufton, J.C., Kupinska, K., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.N.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	106169/Z/14/Z

Revision History  

• Version 1.0: 2019-10-16
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description