Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 66706.59 
• Atom Count: 4025 
• Residue Count: 572 
• Unique protein chains: 1

4YBJ

Type II Dasatinib Analog Crystallized with c-Src Kinase

• DOI: 10.2210/pdb4YBJ/pdb

• Classification: TRANSFERASE
• Organism(s): Gallus gallus
• Expression System: Escherichia coli BL21(DE3)


• 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 
• R-Value Work: 0.218 

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: 10.1021/acschembio.5b01018
• Primary Citation of Related Structures:  
  4YC8, 4YBK


• 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
4A9	A, 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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
4A9	Kd: 0.5 nM (100) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.250 
• R-Value Work: 0.218 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 42.117	α = 90.00
b = 120.062	β = 90.26
c = 63.319	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-02-18 
• 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
  Type: Database references