7XMK

Crystal structure of human RIPK1 kinase domain in complex with compound SKLB923

• PDB DOI: https://doi.org/10.2210/pdb7XMK/pdb

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


• Deposited: 2022-04-26 Released: 2023-04-26 
• Deposition Author(s): Zhang, L., Wang, Y., Li, Y., Yang, S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.259 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 

Literature

Design and synthesis of potent and highly selective inhibitors for the protein kinase RIPK1

Zhang, L., Li, Y., Tian, C., Yang, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 68.18 kDa 
• Atom Count: 4,333 
• Modelled Residue Count: 511 
• 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
PHAROS:  Q13546 GTEx:  ENSG00000137275

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GO4 (Subject of Investigation/LOI)	D [auth A], F [auth B]	5-[2-(cyclopropylcarbonylamino)-[1,2,4]triazolo[1,5-a]pyridin-7-yl]-N-[(1S)-1-(3-fluorophenyl)ethyl]-1-methyl-indole-3-carboxamide C28 H25 F N6 O2 MMHXIUIFLQILFX-INIZCTEOSA-N
IOD	C [auth A], E [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.259 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.885	α = 90
b = 100.904	β = 90
c = 127.594	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-26 
Deposition Author(s): Zhang, L., Wang, Y., Li, Y., Yang, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-04-26
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description