5D9K

Rsk2 N-terminal Kinase in Complex with BI-D1870


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of Potent and Selective RSK Inhibitors as Biological Probes.

Jain, R.Mathur, M.Lan, J.Costales, A.Atallah, G.Ramurthy, S.Subramanian, S.Setti, L.Feucht, P.Warne, B.Doyle, L.Basham, S.Jefferson, A.B.Lindvall, M.Appleton, B.A.Shafer, C.M.

(2015) J.Med.Chem. 58: 6766-6783

  • DOI: 10.1021/acs.jmedchem.5b00450
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • While the p90 ribosomal S6 kinase (RSK) family has been implicated in multiple tumor cell functions, the full understanding of this kinase family has been restricted by the lack of highly selective inhibitors. A bis-phenol pyrazole was identified fro ...

    While the p90 ribosomal S6 kinase (RSK) family has been implicated in multiple tumor cell functions, the full understanding of this kinase family has been restricted by the lack of highly selective inhibitors. A bis-phenol pyrazole was identified from high-throughput screening as an inhibitor of the N-terminal kinase of RSK2. Structure-based drug design using crystallography, conformational analysis, and scaffold morphing resulted in highly optimized difluorophenol pyridine inhibitors of the RSK kinase family as demonstrated cellularly by the inhibition of YB1 phosphorylation. These compounds provide for the first time in vitro tools with an improved selectivity and potency profile to examine the importance of RSK signaling in cancer cells and to fully evaluate RSK as a therapeutic target.


    Related Citations: 
    • Novel potent and selective inhibitors of p90 ribosomal S6 kinase reveal the heterogeneity of RSK function in MAPK-driven cancers.
      Aronchik, I.,Appleton, B.A.,Basham, S.E.,Crawford, K.,Del Rosario, M.,Doyle, L.V.,Estacio, W.F.,Lan, J.,Lindvall, M.K.,Luu, C.A.,Ornelas, E.,Venetsanakos, E.,Shafer, C.M.,Jefferson, A.B.
      (2014) Mol Cancer Res. 12: 803


    Organizational Affiliation

    Global Discovery Chemistry/Oncology & Exploratory Chemistry, Novartis Institutes for Biomedical Research , 5300 Chiron Way, Emeryville, California 94608, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S6 kinase alpha-3
A, B
330Homo sapiensMutation(s): 0 
Gene Names: RPS6KA3 (ISPK1, MAPKAPK1B, RSK2)
EC: 2.7.11.1
Find proteins for P51812 (Homo sapiens)
Go to Gene View: RPS6KA3
Go to UniProtKB:  P51812
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
584
Query on 584

Download SDF File 
Download CCD File 
A, B
(7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7-dimethyl-8-(3-methylbutyl)-7,8-dihydropteridin-6(5H)-one
C19 H23 F2 N5 O2
DTEKTGDVSARYDS-LLVKDONJSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
584IC50: 4 - 24 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 34.190α = 90.00
b = 53.710β = 91.75
c = 207.940γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
BUSTER-TNTrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-08-18 
  • Released Date: 2015-09-02 
  • Deposition Author(s): Appleton, B.A.

Revision History 

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2015-09-23
    Type: Database references