3A4O

Lyn kinase domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.293 

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This is version 1.1 of the entry. See complete history. 


Literature

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: 10.1016/j.bmcl.2009.10.038
  • Primary Citation of Related Structures:  
    3A4O

  • 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 ...

    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.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase LynA [auth X]286Homo sapiensMutation(s): 0 
Gene Names: LYN, JTK8
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P07948 (Homo sapiens)
Explore P07948 
Go to UniProtKB:  P07948
PHAROS:  P07948
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07948
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
STU
Query on STU
Download Ideal Coordinates CCD File 
B [auth X]STAUROSPORINE
C28 H26 N4 O3
HKSZLNNOFSGOKW-FYTWVXJKSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
STU PDBBind:  3A4O IC50: 1.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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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