3WF9

Crystal structure of S6K1 kinase domain in complex with a quinoline derivative 1-oxo-1-[(4-sulfamoylphenyl)amino]propan-2-yl-2-methyl-1,2,3,4-tetrahydroacridine-9-carboxylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

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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 Genomics 15: 153-164

  • DOI: 10.1007/s10969-014-9188-8
  • Primary Citation of Related Structures:  
    3WE4, 3WF5, 3WF6, 3WF7, 3WF8, 3WF9

  • 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 kinase domain in complexes with staurosporine and the S6K1-specific inhibitor PF-4708671 have been reported ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S6 kinase beta-1A329Homo sapiensMutation(s): 0 
Gene Names: RPS6KB1STK14A
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P23443 (Homo sapiens)
Explore P23443 
Go to UniProtKB:  P23443
PHAROS:  P23443
GTEx:  ENSG00000108443 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23443
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FS7
Query on FS7

Download Ideal Coordinates CCD File 
C [auth A](2S)-1-oxo-1-[(4-sulfamoylphenyl)amino]propan-2-yl (2S)-2-methyl-1,2,3,4-tetrahydroacridine-9-carboxylate
C24 H25 N3 O5 S
ZICDFSXBQFNQBM-GJZGRUSLSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
FS7 Binding MOAD:  3WF9 IC50: 567 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.546α = 90
b = 62.331β = 128.18
c = 79.923γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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