Lyn kinase domain

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.293 

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This is version 1.2 of the entry. See complete history


Structural basis for the inhibitor recognition of human Lyn kinase domain

Miyano, N.Kinoshita, T.Nakai, R.Kirii, Y.Yokota, K.Tada, T.

(2009) Bioorg Med Chem Lett 19: 6557-6560

  • DOI: https://doi.org/10.1016/j.bmcl.2009.10.038
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Human Lyn tyrosine kinase is expressed in hematopoietic tissues and plays crucial roles in the signal transduction of hematopoietic immune system. Its excess activity is involved in several tumors. The crystal structure has revealed that the potent inhibitor staurosporine binds to human Lyn kinase domain at the ATP-binding site. The remarkable structural features of the staurosporine-binding region will offer valuable structural insights for the structure-based design of novel Lyn-selective inhibitors.

  • Organizational Affiliation

    Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase LynA [auth X]286Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P07948 (Homo sapiens)
Explore P07948 
Go to UniProtKB:  P07948
PHAROS:  P07948
GTEx:  ENSG00000254087 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07948
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on STU

Download Ideal Coordinates CCD File 
C28 H26 N4 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
STU PDBBind:  3A4O IC50: 1.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.293 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.382α = 90
b = 128.382β = 90
c = 54.875γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data 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: 2009-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description