4YBJ | pdb_00004ybj

Type II Dasatinib Analog Crystallized with c-Src Kinase

• PDB DOI: https://doi.org/10.2210/pdb4YBJ/pdb

• Classification: TRANSFERASE
• Organism(s): Gallus gallus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-02-18 Released: 2016-03-02 
• Deposition Author(s): Kwarcinski, F.E., Brandvold, K.B., Johnson, T.K., Phadke, S., Meagher, J.L., Seeliger, M.A., Stuckey, J.A., Soellner, M.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 
  0.250 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Conformation-Selective Analogues of Dasatinib Reveal Insight into Kinase Inhibitor Binding and Selectivity.

Kwarcinski, F.E., Brandvold, K.R., Phadke, S., Beleh, O.M., Johnson, T.K., Meagher, J.L., Seeliger, M.A., Stuckey, J.A., Soellner, M.B.

(2016) ACS Chem Biol 11: 1296-1304

• PubMed: 26895387 
• DOI: https://doi.org/10.1021/acschembio.5b01018
• Primary Citation Related Structures: 
  4YBJ, 4YBK, 4YC8


• PubMed Abstract: 
  

  In the kinase field, there are many widely held tenets about conformation-selective inhibitors that have yet to be validated using controlled experiments. We have designed, synthesized, and characterized a series of kinase inhibitor analogues of dasatinib, an FDA-approved kinase inhibitor that binds the active conformation. This inhibitor series includes two Type II inhibitors that bind the DFG-out inactive conformation and two inhibitors that bind the αC-helix-out inactive conformation. Using this series of compounds, we analyze the impact that conformation-selective inhibitors have on target binding and kinome-wide selectivity.

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Organizational Affiliation: 
• Department of Pharmacological Sciences, Stony Brook University , Stony Brook, New York 11794, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 66.71 kDa 
• Atom Count: 4,089 
• Modeled Residue Count: 508 
• Deposited Residue Count: 572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	A, B	286	Gallus gallus	Mutation(s): 0  Gene Names: SRC EC: 2.7.10.2
UniProt
Find proteins for P00523 (Gallus gallus) Explore P00523  Go to UniProtKB:  P00523

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4A9	C [auth A], D [auth B]	2-({6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-methylpyrimidin-4-yl}amino)-N-(3-{[3-(trifluoromethyl)benzoyl]amino}phenyl)-1,3-thiazole-5-carboxamide C29 H29 F3 N8 O3 S GWJVXYZDNRXACJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4A9	BindingDB:  4YBJ	Kd: 0.53 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free:  0.250 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.117	α = 90
b = 120.062	β = 90.26
c = 63.319	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
HKL-2000	data collection
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-02 
Deposition Author(s): Kwarcinski, F.E., Brandvold, K.B., Johnson, T.K., Phadke, S., Meagher, J.L., Seeliger, M.A., Stuckey, J.A., Soellner, M.B.

Revision History  

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 1.1: 2016-06-01
  Changes: Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description