4FZ7

Crystal structure of spleen tyrosine kinase complexed with 6-((1R,2S)-2-Amino-cyclohexylamino)-4-(6-ethyl-pyridin-2-ylamino)-pyridazine-3-carboxylic acid amide

• PDB DOI:  https://doi.org/10.2210/pdb4FZ7/pdb

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


• Deposited: 2012-07-06 Released: 2013-07-10 
• Deposition Author(s): Kuglstatter, A., Slade, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.250 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Literature

Using ovality to predict nonmutagenic, orally efficacious pyridazine amides as cell specific spleen tyrosine kinase inhibitors.

Lucas, M.C., Bhagirath, N., Chiao, E., Goldstein, D.M., Hermann, J.C., Hsu, P.Y., Kirchner, S., Kennedy-Smith, J.J., Kuglstatter, A., Lukacs, C., Menke, J., Niu, L., Padilla, F., Peng, Y., Polonchuk, L., Railkar, A., Slade, M., Soth, M., Xu, D., Yadava, P., Yee, C., Zhou, M., Liao, C.

(2014) J Med Chem 57: 2683-2691

• PubMed: 24520947 
• DOI: https://doi.org/10.1021/jm401982j
• Primary Citation of Related Structures:  
  4FZ7


• PubMed Abstract: 
  

Inhibition of spleen tyrosine kinase has attracted much attention as a mechanism for the treatment of cancers and autoimmune diseases such as asthma, rheumatoid arthritis, and systemic lupus erythematous. We report the structure-guided optimization of pyridazine amide spleen tyrosine kinase inhibitors. Early representatives of this scaffold were highly potent and selective but mutagenic in an Ames assay. An approach that led to the successful identification of nonmutagenic examples, as well as further optimization to compounds with reduced cardiovascular liabilities is described. Select pharmacokinetic and in vivo efficacy data are presented.

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Organizational Affiliation: 

Hoffmann-La Roche Inc., pRED, Pharma Research & Early Development, Small Molecule Research, 340 Kingsland Street, Nutley, New Jersey 07110, United States.

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: 2,399 
• Modelled Residue Count: 265 
• 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

Small Molecules

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

Binding Affinity Annotations
ID	Source	Binding Affinity
0VH	BindingDB:  4FZ7	IC50: min: 3.2, max: 79 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.250 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.63	α = 90
b = 84.977	β = 90
c = 88.607	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-10 
Deposition Author(s): Kuglstatter, A., Slade, M.

Revision History  

• Version 1.0: 2013-07-10
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description