3UE4

Structural and spectroscopic analysis of the kinase inhibitor bosutinib binding to the Abl tyrosine kinase domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and spectroscopic analysis of the kinase inhibitor bosutinib and an isomer of bosutinib binding to the abl tyrosine kinase domain.

Levinson, N.M.Boxer, S.G.

(2012) PLoS One 7: e29828-e29828

  • DOI: 10.1371/journal.pone.0029828
  • Primary Citation of Related Structures:  
    3UE4

  • PubMed Abstract: 
  • Chronic myeloid leukemia (CML) is caused by the kinase activity of the BCR-Abl fusion protein. The Abl inhibitors imatinib, nilotinib and dasatinib are currently used to treat CML, but resistance to these inhibitors is a significant clinical problem. ...

    Chronic myeloid leukemia (CML) is caused by the kinase activity of the BCR-Abl fusion protein. The Abl inhibitors imatinib, nilotinib and dasatinib are currently used to treat CML, but resistance to these inhibitors is a significant clinical problem. The kinase inhibitor bosutinib has shown efficacy in clinical trials for imatinib-resistant CML, but its binding mode is unknown. We present the 2.4 Å structure of bosutinib bound to the kinase domain of Abl, which explains the inhibitor's activity against several imatinib-resistant mutants, and reveals that similar inhibitors that lack a nitrile moiety could be effective against the common T315I mutant. We also report that two distinct chemical compounds are currently being sold under the name "bosutinib", and report spectroscopic and structural characterizations of both. We show that the fluorescence properties of these compounds allow inhibitor binding to be measured quantitatively, and that the infrared absorption of the nitrile group reveals a different electrostatic environment in the conserved ATP-binding sites of Abl and Src kinases. Exploiting such differences could lead to inhibitors with improved selectivity.


    Organizational Affiliation

    Department of Chemistry, Stanford University, Stanford, California, United States of America. nickl@stanford.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase ABL1AB287Homo sapiensMutation(s): 0 
Gene Names: ABL1ABLJTK7
EC: 2.7.10.2
Find proteins for P00519 (Homo sapiens)
Explore P00519 
Go to UniProtKB:  P00519
NIH Common Fund Data Resources
PHAROS  P00519
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DB8
Query on DB8

Download Ideal Coordinates CCD File 
A, B
4-[(2,4-dichloro-5-methoxyphenyl)amino]-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinoline-3-carbonitrile
C26 H29 Cl2 N5 O3
UBPYILGKFZZVDX-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DB8IC50:  0.5   nM  BindingDB
DB8Kd:  0.18000000715255737   nM  BindingDB
DB8IC50:  1.100000023841858   nM  BindingDB
DB8Kd:  0.10999999940395355   nM  BindingDB
DB8Kd:  0.029999999329447746   nM  BindingDB
DB8Kd:  0.11999999731779099   nM  BindingDB
DB8Kd:  3.5999999046325684   nM  BindingDB
DB8IC50 :  1.100000023841858   nM  PDBBind
DB8Kd:  21   nM  BindingDB
DB8Kd:  0.6299999952316284   nM  BindingDB
DB8IC50:  1   nM  BindingDB
DB8Kd:  0.09000000357627869   nM  BindingDB
DB8IC50:  0.5   nM  BindingDB
DB8Kd:  0.05999999865889549   nM  BindingDB
DB8Kd:  0.05000000074505806   nM  BindingDB
DB8IC50:  1.100000023841858   nM  BindingDB
DB8Kd:  0.03999999910593033   nM  BindingDB
DB8Kd:  1.5   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.192 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.86α = 90
b = 113.76β = 90
c = 127.64γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-18
    Type: Initial release
  • Version 1.1: 2012-04-25
    Changes: Database references