3QUP | pdb_00003qup

Inhibitor bound structure of the kinase domain of the murine receptor tyrosine kinase TYRO3 (Sky)

• PDB DOI: https://doi.org/10.2210/pdb3QUP/pdb

• Classification: Transferase/transferase inhibitor
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2011-02-24 Released: 2011-12-21 
• Deposition Author(s): Ohren, J.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Literature

Novel and selective spiroindoline-based inhibitors of sky kinase.

Powell, N.A., Kohrt, J.T., Filipski, K.J., Kaufman, M., Sheehan, D., Edmunds, J.E., Delaney, A., Wang, Y., Bourbonais, F., Lee, D.Y., Schwende, F., Sun, F., McConnell, P., Catana, C., Chen, H., Ohren, J., Perrin, L.A.

(2012) Bioorg Med Chem Lett 22: 190-193

• PubMed: 22119469 
• DOI: https://doi.org/10.1016/j.bmcl.2011.11.036
• Primary Citation of Related Structures:  
  3QUP


• PubMed Abstract: 
  

  We report the discovery of a novel series of spiroindoline-based inhibitors of Sky kinase that bind in the ATP-binding site and exhibit high levels of kinome selectivity through filling the Ala571-subpocket. These inhibitors exhibit moderate oral bioavailability in the rat due to low absorption across the gut wall.

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Organizational Affiliation: 

Pfizer Global Research & Development, Michigan Laboratories, Ann Arbor, MI 48105, USA. [e-mail]

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: 37.19 kDa 
• Atom Count: 2,023 
• Modelled Residue Count: 241 
• Deposited Residue Count: 323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase receptor TYRO3	A	323	Mus musculus	Mutation(s): 0  Gene Names: Tyro3, Dtk, Rse EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P55144 (Mus musculus) Explore P55144  Go to UniProtKB:  P55144
IMPC:  MGI:104294

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LUN	B [auth A]	(5-fluoro-1H-indol-2-yl)[(3R)-1'-[(3R)-piperidin-3-yl]spiro[indole-3,3'-pyrrolidin]-1(2H)-yl]methanone C25 H27 F N4 O ABNVVKAVWJYHCL-KBMIEXCESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.986	α = 90
b = 57.343	β = 100.3
c = 60.562	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-21 
Deposition Author(s): Ohren, J.F.

Revision History  

• Version 1.0: 2011-12-21
  Type: Initial release
  
• Version 1.1: 2012-01-11
  Changes: Database references
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations