3F6X

c-Src kinase domain in complex with small molecule inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Tuning a three-component reaction for trapping kinase substrate complexes.

Statsuk, A.V.Maly, D.J.Seeliger, M.A.Fabian, M.A.Biggs, W.H.Lockhart, D.J.Zarrinkar, P.P.Kuriyan, J.Shokat, K.M.

(2008) J Am Chem Soc 130: 17568-17574

  • DOI: 10.1021/ja807066f
  • Primary Citation of Related Structures:  
    3F6X

  • PubMed Abstract: 
  • The upstream protein kinases responsible for thousands of phosphorylation events in the phosphoproteome remain to be discovered. We developed a three-component chemical reaction which converts the transient noncovalent substrate-kinase complex into a covalently cross-linked product by utilizing a dialdehyde-based cross-linker, 1 ...

    The upstream protein kinases responsible for thousands of phosphorylation events in the phosphoproteome remain to be discovered. We developed a three-component chemical reaction which converts the transient noncovalent substrate-kinase complex into a covalently cross-linked product by utilizing a dialdehyde-based cross-linker, 1. Unfortunately, the reaction of 1 with a lysine in the kinase active site and an engineered cysteine on the substrate to form an isoindole cross-linked product could not be performed in the presence of competing cellular proteins due to nonspecific side reactions. In order to more selectively target the cross-linker to protein kinases in cell lysates, we replaced the weak, kinase-binding adenosine moiety of 1 with a potent protein kinase inhibitor scaffold. In addition, we replaced the o-phthaldialdehyde moiety in 1 with a less-reactive thiophene-2,3-dicarboxaldehyde moiety. The combination of these two structural modifications provides for cross-linking of a cysteine-containing substrate to its corresponding kinase in the presence of competing cellular proteins.


    Organizational Affiliation

    Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94107, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase Src ABCD286Gallus gallusMutation(s): 0 
Gene Names: SRC
EC: 2.7.10.2
Find proteins for P00523 (Gallus gallus)
Explore P00523 
Go to UniProtKB:  P00523
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHH
Query on IHH

Download Ideal Coordinates CCD File 
A, B, C, D
[4-({4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]quinazolin-2-yl}amino)phenyl]acetonitrile
C22 H19 N7
NVMCVWOODOWOLT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.234 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.697α = 89.06
b = 74.488β = 89.97
c = 84.652γ = 78.43
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance