4EQU

Human STK-10 (LOK) kinase domain in DFG-out conformation with inhibitor DSA-7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Affinity-Based Probes Based on Type II Kinase Inhibitors.

Ranjitkar, P.Perera, B.G.Swaney, D.L.Hari, S.B.Larson, E.T.Krishnamurty, R.Merritt, E.A.Villen, J.Maly, D.J.

(2012) J.Am.Chem.Soc. 134: 19017-19025

  • DOI: 10.1021/ja306035v

  • PubMed Abstract: 
  • Protein kinases are key components of most mammalian signal transduction networks and are therapeutically relevant drug targets. Efforts to study protein kinase function would benefit from new technologies that are able to profile kinases in complex ...

    Protein kinases are key components of most mammalian signal transduction networks and are therapeutically relevant drug targets. Efforts to study protein kinase function would benefit from new technologies that are able to profile kinases in complex proteomes. Here, we describe active site-directed probes for profiling kinases in whole cell extracts and live cells. These probes contain general ligands that stabilize a specific inactive conformation of the ATP-binding sites of protein kinases, as well as trifluoromethylphenyl diazirine and alkyne moieties that allow covalent modification and enrichment of kinases, respectively. A diverse group of serine/threonine and tyrosine kinases were identified as specific targets of these probes in whole cell extracts. In addition, a number of kinase targets were selectively labeled in live cells. Our chemical proteomics approach should be valuable for interrogating protein kinase active sites in physiologically relevant environments.


    Organizational Affiliation

    Department of Chemistry, University of Washington, Seattle, Washington 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase 10
A, B
302Homo sapiensMutation(s): 0 
Gene Names: STK10 (LOK)
EC: 2.7.11.1
Find proteins for O94804 (Homo sapiens)
Go to Gene View: STK10
Go to UniProtKB:  O94804
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
G6I
Query on G6I

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Download CCD File 
A, B
N-{3-[(3-{4-[(4-methoxyphenyl)amino]-1,3,5-triazin-2-yl}pyridin-2-yl)amino]-4-methylphenyl}-3-(trifluoromethyl)benzamide
C30 H24 F3 N7 O2
FLZNVZVIUIDCOF-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

Download SDF File 
Download CCD File 
B
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 61.810α = 90.00
b = 49.040β = 101.42
c = 133.760γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
BALBESphasing
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-07
    Type: Initial release
  • Version 1.1: 2012-11-14
    Type: Structure summary
  • Version 1.2: 2012-12-19
    Type: Database references