3F3T

Kinase domain of cSrc in complex with inhibitor RL38 (Type III)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A new screening assay for allosteric inhibitors of cSrc

Simard, J.R.Kluter, S.Grutter, C.Getlik, M.Rabiller, M.Rode, H.B.Rauh, D.

(2009) Nat.Chem.Biol. 5: 394-396

  • DOI: 10.1038/nchembio.162
  • Primary Citation of Related Structures:  3F3U

  • PubMed Abstract: 
  • Targeting kinases outside the highly conserved ATP pocket is thought to be a promising strategy for overcoming bottlenecks in kinase inhibitor research, such as limited selectivity and drug resistance. Here we report the development and application o ...

    Targeting kinases outside the highly conserved ATP pocket is thought to be a promising strategy for overcoming bottlenecks in kinase inhibitor research, such as limited selectivity and drug resistance. Here we report the development and application of a direct binding assay to detect small molecules that stabilize the inactive conformation of the tyrosine kinase cSrc. Protein X-ray crystallography validated the assay results and confirmed an exclusively allosteric binding mode.


    Organizational Affiliation

    Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene tyrosine-protein kinase Src
A, B
286Gallus gallusGene 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
1AU
Query on 1AU

Download SDF File 
Download CCD File 
A
1-[1-(3-aminophenyl)-3-tert-butyl-1H-pyrazol-5-yl]-3-naphthalen-1-ylurea
1-[2-(3-Amino-phenyl)-5-tert-butyl-2H-pyrazol-3-yl]-3-naphthalen-1-yl-urea
C24 H25 N5 O
HJWMLCDGRWWLAQ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1AUIC50: 64100 nM (99) BINDINGDB
1AUIC50: 64100 nM BINDINGMOAD
1AUKd: 26000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.244 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 42.010α = 78.71
b = 63.490β = 89.71
c = 74.990γ = 89.91
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata scaling
XSCALEdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance