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

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1038/nchembio.162
  • Primary Citation of Related Structures:  
    3F3T, 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase Src
A, B
286Gallus gallusMutation(s): 1 
Find proteins for P00523 (Gallus gallus)
Explore P00523 
Go to UniProtKB:  P00523
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00523
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 1AU

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
C24 H25 N5 O
Binding Affinity Annotations 
IDSourceBinding Affinity
1AU PDBBind:  3F3T Kd: 2.60e+4 (nM) from 1 assay(s)
Binding MOAD:  3F3T Kd: 2.60e+4 (nM) from 1 assay(s)
BindingDB:  3F3T IC50: 6.41e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.01α = 78.71
b = 63.49β = 89.71
c = 74.99γ = 89.91
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-01
    Changes: Data collection, Refinement description