4GFG

Crystal structure of spleen tyrosine kinase complexed with r9021

• PDB DOI: https://doi.org/10.2210/pdb4GFG/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2012-08-03 Released: 2013-08-14 
• Deposition Author(s): Lukacs, C., Slade, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.246 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 

Starting Model: experimental

Literature

A specific SYK inhibitor blocks B Cell Receptor, Fc Receptor, and Toll-like Receptor 9 pathways for the treatment of inflammatory diseases.

Hsu, J., Kim, Y., Hu, D.-Q., Xu, D., Zhang, J., Pashine, A., Menke, J., Whittard, T., Romero, N., Truitt, T., Lukacs, C., Zhou, M., Lucas, M., Slade, M., DeMartino, J., Tan, S.-L., Liao, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 34.24 kDa 
• Atom Count: 2,379 
• Modelled Residue Count: 277 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase SYK	A	291	Homo sapiens	Mutation(s): 0  Gene Names: SYK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P43405 (Homo sapiens) Explore P43405  Go to UniProtKB:  P43405
PHAROS:  P43405 GTEx:  ENSG00000165025

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0XF	B [auth A]	6-{[(1R,2S)-2-aminocyclohexyl]amino}-4-[(5,6-dimethylpyridin-2-yl)amino]pyridazine-3-carboxamide C18 H25 N7 O XJZVCDVZCRLIKN-QWHCGFSZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0XF	BindingDB:  4GFG	IC50: min: 5, max: 32 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.246 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.061	α = 90
b = 85.647	β = 90
c = 90.93	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
CNX	refinement
XDS	data reduction
SCALA	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-14 
Deposition Author(s): Lukacs, C., Slade, M.

Revision History  

• Version 1.0: 2013-08-14
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description