4YBK

C-Helix-Out Dasatinib Analog Crystallized with c-Src Kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1021/acschembio.5b01018
  • Primary Citation of Related Structures:  

  • 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 dasa ...

    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.


    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
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene tyrosine-protein kinase Src
A
286Gallus gallusMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4B7
Query on 4B7

Download SDF File 
Download CCD File 
A
2-({6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-methylpyrimidin-4-yl}amino)-N-(4-phenoxyphenyl)-1,3-thiazole-5-carboxamide
C27 H29 N7 O3 S
QUFCHHSHOLSVOT-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4B7Kd: 15 nM (100) BINDINGDB
4B7Kd: 15 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 41.334α = 90.00
b = 62.213β = 90.00
c = 102.803γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHASERphasing
BUSTER-TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-06-01
    Type: Database references