3UBD

Structure of N-terminal domain of RSK2 kinase in complex with flavonoid glycoside SL0101


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Insights into the Inhibition of the p90 Ribosomal S6 Kinase (RSK) by the Flavonol Glycoside SL0101 from the 1.5 A Crystal Structure of the N-Terminal Domain of RSK2 with Bound Inhibitor.

Utepbergenov, D.Derewenda, U.Olekhnovich, N.Szukalska, G.Banerjee, B.Hilinski, M.K.Lannigan, D.A.Stukenberg, P.T.Derewenda, Z.S.

(2012) Biochemistry 51: 6499-6510

  • DOI: 10.1021/bi300620c
  • Primary Citation of Related Structures:  4EL9

  • PubMed Abstract: 
  • The p90 ribosomal S6 family of kinases (RSK) are potential drug targets, due to their involvement in cancer and other pathologies. There are currently only two known selective inhibitors of RSK, but the basis for selectivity is not known. One of thes ...

    The p90 ribosomal S6 family of kinases (RSK) are potential drug targets, due to their involvement in cancer and other pathologies. There are currently only two known selective inhibitors of RSK, but the basis for selectivity is not known. One of these inhibitors is a naturally occurring kaempferol-α-L-diacetylrhamnoside, SL0101. Here, we report the crystal structure of the complex of the N-terminal kinase domain of the RSK2 isoform with SL0101 at 1.5 Å resolution. The refined atomic model reveals unprecedented structural reorganization of the protein moiety, as compared to the nucleotide-bound form. The entire N-lobe, the hinge region, and the αD-helix undergo dramatic conformational changes resulting in a rearrangement of the nucleotide binding site with concomitant formation of a highly hydrophobic pocket spatially suited to accommodate SL0101. These unexpected results will be invaluable in further optimization of the SL0101 scaffold as a promising lead for a novel class of kinase inhibitors.


    Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, School of Medicine, Charlottesville, VA 22908, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S6 kinase alpha-3
A
304Mus musculusGene Names: Rps6ka3 (Mapkapk1b, Rps6ka-rs1, Rsk2)
EC: 2.7.11.1
Find proteins for P18654 (Mus musculus)
Go to UniProtKB:  P18654
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SL0
Query on SL0

Download SDF File 
Download CCD File 
A
5,7-dihydroxy-2-(4-hydroxyphenyl)-4-oxo-4H-chromen-3-yl 3,4-di-O-acetyl-6-deoxy-alpha-L-mannopyranoside
SL 0101-1
C25 H24 O12
SXOZSDJHGMAEGZ-IGKKHSBFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SL0Kd: 2900 nM BINDINGMOAD
SL0Kd: 2900 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 98.446α = 90.00
b = 40.700β = 114.54
c = 83.354γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SERGUIdata collection
MOLREPphasing
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Advisory, Refinement description