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

Experimental Data Snapshot

  • Resolution: 1.53 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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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: https://doi.org/10.1021/bi300620c
  • Primary Citation of Related Structures:  
    3UBD, 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S6 kinase alpha-3304Mus musculusMutation(s): 0 
Gene Names: Mapkapk1bRps6ka-rs1Rps6ka3Rsk2
Find proteins for P18654 (Mus musculus)
Explore P18654 
Go to UniProtKB:  P18654
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18654
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SL0

Download Ideal Coordinates CCD File 
B [auth A]5,7-dihydroxy-2-(4-hydroxyphenyl)-4-oxo-4H-chromen-3-yl 3,4-di-O-acetyl-6-deoxy-alpha-L-mannopyranoside
C25 H24 O12
Binding Affinity Annotations 
IDSourceBinding Affinity
SL0 Binding MOAD:  3UBD Kd: 2900 (nM) from 1 assay(s)
PDBBind:  3UBD Kd: 2900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.53 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.446α = 90
b = 40.7β = 114.54
c = 83.354γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
SERGUIdata collection
DENZOdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Advisory, Refinement description
  • Version 1.2: 2023-09-13
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description