4GFG

Crystal structure of spleen tyrosine kinase complexed with r9021

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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


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.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase SYK291Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43405
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0XF
Query on 0XF
Download Ideal Coordinates CCD File 
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 
IDSourceBinding 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 = 40.061α = 90
b = 85.647β = 90
c = 90.93γ = 90
Software Package:
Software NamePurpose
CCP4model building
CNXrefinement
XDSdata reduction
SCALAdata scaling
CCP4phasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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