4EQU

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    4EQU

  • 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 proteomes ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase 10A, B302Homo sapiensMutation(s): 0 
Gene Names: STK10LOK
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O94804 (Homo sapiens)
Explore O94804 
Go to UniProtKB:  O94804
PHAROS:  O94804
GTEx:  ENSG00000072786 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94804
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G6I
Query on G6I

Download Ideal Coordinates CCD File 
C [auth A],
F [auth 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 Ideal Coordinates CCD File 
J [auth B]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
G [auth B],
H [auth B],
I [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.81α = 90
b = 49.04β = 101.42
c = 133.76γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
BALBESphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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