4FF8 | pdb_00004ff8

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

• PDB DOI: https://doi.org/10.2210/pdb4FF8/pdb

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


• Deposited: 2012-05-31 Released: 2013-03-13 
• Deposition Author(s): Ohren, J.F., Powell, N.A., Kohrt, J., Perrin, L.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.324 (Depositor), 0.316 (DCC) 
• R-Value Work: 
  0.277 (Depositor), 0.274 (DCC) 
• R-Value Observed: 
  0.279 (Depositor) 

Literature

Highly selective 2,4-diaminopyrimidine-5-carboxamide inhibitors of Sky kinase.

Powell, N.A., Hoffman, J.K., Ciske, F.L., Kaufman, M.D., Kohrt, J.T., Quin, J., Sheehan, D.J., Delaney, A., Baxi, S.M., Catana, C., McConnell, P., Ohren, J., Perrin, L.A., Edmunds, J.J.

(2013) Bioorg Med Chem Lett 23: 1046-1050

• PubMed: 23312472 
• DOI: https://doi.org/10.1016/j.bmcl.2012.12.013
• Primary Citation Related Structures: 
  4FEQ, 4FF8


• PubMed Abstract: 
  

  We report the SAR around a series of 2,4-diaminopyrimidine-5-carboxamide inhibitors of Sky kinase. 2-Aminophenethyl analogs demonstrate excellent potency but moderate kinase selectivity, while 2-aminobenzyl analogs that fill the Ala571 subpocket exhibit good inhibition activity and excellent kinase selectivity.

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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: 37.24 kDa 
• Atom Count: 1,400 
• Modeled Residue Count: 169 
• 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
14S	B [auth A]	4-(cyclopentylamino)-2-[(2-methoxybenzyl)amino]-N-[3-(2-oxopyrrolidin-1-yl)propyl]pyrimidine-5-carboxamide C25 H34 N6 O3 ZXZLVQGNVOKCAS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
14S	BindingDB:  4FF8	IC50: 400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.324 (Depositor), 0.316 (DCC) 
• R-Value Work:  0.277 (Depositor), 0.274 (DCC) 
• R-Value Observed: 0.279 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.522	α = 90
b = 57.245	β = 100.85
c = 60.076	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-13 
Deposition Author(s): Ohren, J.F., Powell, N.A., Kohrt, J., Perrin, L.A.

Revision History  

• Version 1.0: 2013-03-13
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations