3WF6

Crystal structure of S6K1 kinase domain in complex with a pyrazolopyrimidine derivative 4-[4-(1H-indol-3-yl)-3,6-dihydropyridin-1(2H)-yl]-1H-pyrazolo[3,4-d]pyrimidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.031 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of the S6K1 kinase domain in complexes with inhibitors

Niwa, H.Mikuni, J.Sasaki, S.Tomabechi, Y.Honda, K.Ikeda, M.Ohsawa, N.Wakiyama, M.Handa, N.Shirouzu, M.Honma, T.Tanaka, A.Yokoyama, S.

(2014) J.Struct.Funct.Genom. 15: 153-164

  • DOI: 10.1007/s10969-014-9188-8
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ribosomal protein S6 kinase 1 (S6K1) is a serine/threonine protein kinase that plays an important role in the PIK3/mTOR signaling pathway, and is implicated in diseases including diabetes, obesity, and cancer. The crystal structures of the S6K1 kinas ...

    Ribosomal protein S6 kinase 1 (S6K1) is a serine/threonine protein kinase that plays an important role in the PIK3/mTOR signaling pathway, and is implicated in diseases including diabetes, obesity, and cancer. The crystal structures of the S6K1 kinase domain in complexes with staurosporine and the S6K1-specific inhibitor PF-4708671 have been reported. In the present study, five compounds (F108, F109, F176, F177, and F179) were newly identified by in silico screening of a chemical library and kinase assay. The crystal structures of the five inhibitors in complexes with the S6K1 kinase domain were determined at resolutions between 1.85 and 2.10 Å. All of the inhibitors bound to the ATP binding site, lying along the P-loop, while the activation loop stayed in the inactive form. Compound F179, with a carbonyl group in the middle of the molecule, altered the αC helix conformation by interacting with the invariant Lys123. Compounds F176 and F177 bound slightly distant from the hinge region, and their sulfoamide groups formed polar interactions with the protein. The structural features required for the specific binding of inhibitors are discussed.


    Organizational Affiliation

    RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S6 kinase beta-1
A
329Homo sapiensMutation(s): 0 
Gene Names: RPS6KB1 (STK14A)
EC: 2.7.11.1
Find proteins for P23443 (Homo sapiens)
Go to Gene View: RPS6KB1
Go to UniProtKB:  P23443
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FZ9
Query on FZ9

Download SDF File 
Download CCD File 
A
4-[4-(1H-indol-3-yl)-3,6-dihydropyridin-1(2H)-yl]-1H-pyrazolo[3,4-d]pyrimidine
C18 H16 N6
QOXYIHCPHZOWJH-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FZ9IC50: 33 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.031 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.195 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 69.073α = 90.00
b = 69.073β = 90.00
c = 144.983γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2014-08-13
    Type: Database references
  • Version 1.2: 2014-10-29
    Type: Database references