LCK bound to imatinib

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

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Classifying protein kinase structures guides use of ligand-selectivity profiles to predict inactive conformations: Structure of lck/imatinib complex.

Jacobs, M.D.Caron, P.R.Hare, B.J.

(2007) Proteins 70: 1451-1460

  • DOI: https://doi.org/10.1002/prot.21633
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    We report a clustering of public human protein kinase structures based on the conformations of two structural elements, the activation segment and the C-helix, revealing three discrete clusters. One cluster includes kinases in catalytically active conformations. Each of the other clusters contains a distinct inactive conformation. Typically, kinases adopt at most one of the inactive conformations in available X-ray structures, implying that one of the conformations is preferred for many kinases. The classification is consistent with selectivity profiles of several well-characterized kinase inhibitors. We show further that inhibitor selectivity profiles guide kinase classification. For example, selective inhibition of lck among src-family kinases by imatinib (Gleevec) suggests that the relative stabilities of inactive conformations of lck are different from other src-family kinases. We report the X-ray structure of the lck/imatinib complex, confirming that the conformation adopted by lck is distinct from other structurally-characterized src-family kinases and instead resembles kinases abl1 and kit in complex with imatinib. Our classification creates new paths for designing small-molecule inhibitors.

  • Organizational Affiliation

    Vertex Pharmaceuticals Incorporated, 130 Waverly Street, Cambridge, Massachusetts 02139, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase LCK289Homo sapiensMutation(s): 0 
Gene Names: LCK
UniProt & NIH Common Fund Data Resources
Find proteins for P06239 (Homo sapiens)
Explore P06239 
Go to UniProtKB:  P06239
GTEx:  ENSG00000182866 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06239
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on STI

Download Ideal Coordinates CCD File 
C29 H31 N7 O
Binding Affinity Annotations 
IDSourceBinding Affinity
STI BindingDB:  2PL0 Ki: 6893 (nM) from 1 assay(s)
Kd: min: 40, max: 62 (nM) from 2 assay(s)
IC50: min: 160, max: 320 (nM) from 2 assay(s)
PDBBind:  2PL0 Kd: 62 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.21α = 90
b = 103.17β = 90
c = 52.33γ = 90
Software Package:
Software NamePurpose
d*TREKdata processing
PDB_EXTRACTdata extraction
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2007-10-09 
  • Deposition Author(s): Jacobs, M.D.

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Structure summary