3KXZ

The complex crystal structure of LCK with a probe molecule w259


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Novel synthesis and structural characterization of a high-affinity paramagnetic kinase probe for the identification of non-ATP site binders by nuclear magnetic resonance.

Moy, F.J.Lee, A.Gavrin, L.K.Xu, Z.B.Sievers, A.Kieras, E.Stochaj, W.Mosyak, L.McKew, J.Tsao, D.H.

(2010) J.Med.Chem. 53: 1238-1249

  • DOI: 10.1021/jm901525b

  • PubMed Abstract: 
  • To aid in the pursuit of selective kinase inhibitors, we have developed a unique ATP site binder tool for the detection of binders outside the ATP site by nuclear magnetic resonance (NMR). We report here the novel synthesis that led to this paramagne ...

    To aid in the pursuit of selective kinase inhibitors, we have developed a unique ATP site binder tool for the detection of binders outside the ATP site by nuclear magnetic resonance (NMR). We report here the novel synthesis that led to this paramagnetic spin-labeled pyrazolopyrimidine probe (1), which exhibits nanomolar inhibitory activity against multiple kinases. We demonstrate the application of this probe by performing NMR binding experiments with Lck and Src kinases and utilize it to detect the binding of two compounds proximal to the ATP site. The complex structure of the probe with Lck is also presented, revealing how the probe fits in the ATP site and the specific interactions it has with the protein. We believe that this spin-labeled probe is a valuable tool that holds broad applicability in a screen for non-ATP site binders.


    Organizational Affiliation

    Structural Biology and Computational Chemistry, Wyeth Research, 200 CambridgePark Drive, Cambridge, Massachusetts 02140, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene tyrosine-protein kinase LCK
A
287Homo sapiensMutation(s): 0 
Gene Names: LCK
EC: 2.7.10.2
Find proteins for P06239 (Homo sapiens)
Go to Gene View: LCK
Go to UniProtKB:  P06239
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
925
Query on 925

Download SDF File 
Download CCD File 
A
3-[7-[(3-hydroxyphenyl)amino]pyrazolo[1,5-a]pyrimidin-2-yl]-N-(1-hydroxy-2,2,6,6-tetramethyl-piperidin-4-yl)benzamide
N-(1-hydroxy-2,2,6,6-tetramethylpiperidin-4-yl)-3-(7-(3-hydroxyphenylamino)pyrazolo[1,5-a]pyrimidin-2-yl)benzamide
C28 H32 N6 O3
WZEJOLDIQBJKQR-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PTRKd: 400000 nM (100) BINDINGDB
925IC50: 35 nM BINDINGMOAD
925IC50: 35 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.012α = 90.00
b = 73.784β = 90.00
c = 84.717γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
PHENIXrefinement
ADSCdata collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance