6S1F | pdb_00006s1f

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free:
0.300 (Depositor), 0.278 (DCC)
R-Value Work:
0.254 (Depositor)
R-Value Observed:
0.256 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O43353
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free: 0.300 (Depositor), 0.278 (DCC)
R-Value Work: 0.254 (Depositor)
R-Value Observed: 0.256 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-10-16

Deposition Author(s):

Burgess-Brown, N.A.

Arrowsmith, C.H.

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

Revision History (Full details and data files)

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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.