2ZV9

Lyn Tyrosine Kinase Domain-PP2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structures of the Lyn Protein Tyrosine Kinase Domain in Its Apo- and Inhibitor-bound State

Williams, N.K.Lucet, I.S.Klinken, S.P.Ingley, E.Rossjohn, J.

(2009) J Biol Chem 284: 284-291

  • DOI: 10.1074/jbc.M807850200
  • Primary Citation of Related Structures:  
    2ZV7, 2ZV8, 2ZV9, 2ZVA

  • PubMed Abstract: 
  • The Src-family protein-tyrosine kinase (PTK) Lyn is the most important Src-family kinase in B cells, having both inhibitory and stimulatory activity that is dependent on the receptor, ligand, and developmental context of the B cell. An important role for Lyn has been reported in acute myeloid leukemia and chronic myeloid leukemia, as well as certain solid tumors ...

    The Src-family protein-tyrosine kinase (PTK) Lyn is the most important Src-family kinase in B cells, having both inhibitory and stimulatory activity that is dependent on the receptor, ligand, and developmental context of the B cell. An important role for Lyn has been reported in acute myeloid leukemia and chronic myeloid leukemia, as well as certain solid tumors. Although several Src-family inhibitors are available, the development of Lyn-specific inhibitors, or inhibitors with reduced off-target activity to Lyn, has been hampered by the lack of structural data on the Lyn kinase. Here we report the crystal structure of the non-liganded form of Lyn kinase domain, as well as in complex with three different inhibitors: the ATP analogue AMP-PNP; the pan Src kinase inhibitor PP2; and the BCR-Abl/Src-family inhibitor Dasatinib. The Lyn kinase domain was determined in its "active" conformation, but in the unphosphorylated state. All three inhibitors are bound at the ATP-binding site, with PP2 and Dasatinib extending into a hydrophobic pocket deep in the substrate cleft, thereby providing a basis for the Src-specific inhibition. Analysis of sequence and structural differences around the active site region of the Src-family PTKs were evident. Accordingly, our data provide valuable information for the further development of therapeutics targeting Lyn and the important Src-family of kinases.


    Organizational Affiliation

    Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase LynA279Mus musculusMutation(s): 0 
Gene Names: Lyn
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P25911 (Mus musculus)
Explore P25911 
Go to UniProtKB:  P25911
IMPC:  MGI:96892
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PP2 (Subject of Investigation/LOI)
Query on PP2

Download Ideal Coordinates CCD File 
B [auth A]1-TERT-BUTYL-3-(4-CHLORO-PHENYL)-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-YLAMINE
C15 H17 Cl N5
PBBRWFOVCUAONR-UHFFFAOYSA-O
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
PP2 PDBBind:  2ZV9 IC50: 9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.468α = 90
b = 128.468β = 90
c = 54.169γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance