4MXX

Human Src A403T mutant bound to kinase inhibitor bosutinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A conserved water-mediated hydrogen bond network defines bosutinib's kinase selectivity.

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

(2014) Nat.Chem.Biol. 10: 127-132

  • DOI: 10.1038/nchembio.1404
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Kinase inhibitors are important cancer drugs, but they tend to display limited target specificity, and their target profiles are often challenging to rationalize in terms of molecular mechanism. Here we report that the clinical kinase inhibitor bosut ...

    Kinase inhibitors are important cancer drugs, but they tend to display limited target specificity, and their target profiles are often challenging to rationalize in terms of molecular mechanism. Here we report that the clinical kinase inhibitor bosutinib recognizes its kinase targets by engaging a pair of conserved structured water molecules in the active site and that many other kinase inhibitors share a similar recognition mechanism. Using the nitrile group of bosutinib as an infrared probe, we show that the gatekeeper residue and one other position in the ATP-binding site control access of the drug to the structured water molecules and that the amino acids found at these positions account for the kinome-wide target spectrum of the drug. Our work highlights the importance of structured water molecules for inhibitor recognition, reveals a new role for the kinase gatekeeper and showcases an effective approach for elucidating the molecular origins of selectivity patterns.


    Organizational Affiliation

    Department of Chemistry, Stanford University, Stanford, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene tyrosine-protein kinase Src
A, B
286Homo sapiensMutation(s): 1 
Gene Names: SRC (SRC1)
EC: 2.7.10.2
Find proteins for P12931 (Homo sapiens)
Go to Gene View: SRC
Go to UniProtKB:  P12931
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DB8
Query on DB8

Download SDF File 
Download CCD File 
A, B
4-[(2,4-dichloro-5-methoxyphenyl)amino]-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinoline-3-carbonitrile
Bosutinib
C26 H29 Cl2 N5 O3
UBPYILGKFZZVDX-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DB8IC50: 0.4 - 100 nM (89) BINDINGDB
DB8Kd: 1 - 4 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.206 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 41.780α = 79.47
b = 63.050β = 89.19
c = 73.770γ = 90.02
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXrefinement
SCALAdata scaling
PHASERphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-04
    Type: Initial release
  • Version 1.1: 2014-02-05
    Type: Database references