8I2N

The RIPK1 kinase domain in complex with QY7-2B compound

• PDB DOI: https://doi.org/10.2210/pdb8I2N/pdb

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


• Deposited: 2023-01-14 Released: 2024-01-31 
• Deposition Author(s): Gong, X.Y., Li, Y., Meng, H.Y., Pan, L.F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.245 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 

Starting Model: experimental

Literature

The RIPK1 kinase domain in complex with QY7-2B compound

Gong, X.Y., Li, Y., Meng, H.Y., Pan, L.F.

To be published.

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: 67.89 kDa 
• Atom Count: 4,415 
• Modelled Residue Count: 537 
• Deposited Residue Count: 588 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-interacting serine/threonine-protein kinase 1	A, B	294	Homo sapiens	Mutation(s): 4  Gene Names: RIPK1, RIP, RIP1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13546 (Homo sapiens) Explore Q13546  Go to UniProtKB:  Q13546
GTEx:  ENSG00000137275

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O4U (Subject of Investigation/LOI)	C [auth A], D [auth B]	~{N}-methyl-1-[4-[[[1-methyl-5-(phenylmethyl)pyrazol-3-yl]carbonylamino]methyl]phenyl]benzimidazole-5-carboxamide C28 H26 N6 O2 OVVBAKUOCIBISQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.245 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.51	α = 90
b = 98.742	β = 90
c = 128.129	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-31 
Deposition Author(s): Gong, X.Y., Li, Y., Meng, H.Y., Pan, L.F.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21822705

Revision History  

• Version 1.0: 2024-01-31
  Type: Initial release