4C37

PKA-S6K1 Chimera with compound 21a (CCT196539) bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Discovery of Potent Ribosomal S6 Kinase Inhibitors by High-Throughput Screening and Structure-Guided Drug Design.

Couty, S.Westwood, I.M.Kalusa, A.Cano, C.Travers, J.Boxall, K.Chow, C.L.Burns, S.Schmitt, J.Pickard, L.Barillari, C.Mcandrew, P.C.Clarke, P.A.Linardopoulos, S.Griffin, R.J.Aherne, G.W.Raynaud, F.I.Workman, P.Jones, K.Van Montfort, R.L.M.

(2013) Oncotarget 4: 1647

  • DOI: 10.18632/oncotarget.1255
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The ribosomal P70 S6 kinases play a crucial role in PI3K/mTOR regulated signalling pathways and are therefore potential targets for the treatment of a variety of diseases including diabetes and cancer. In this study we describe the identification of ...

    The ribosomal P70 S6 kinases play a crucial role in PI3K/mTOR regulated signalling pathways and are therefore potential targets for the treatment of a variety of diseases including diabetes and cancer. In this study we describe the identification of three series of chemically distinct S6K1 inhibitors. In addition, we report a novel PKA-S6K1 chimeric protein with five mutations in or near its ATP-binding site, which was used to determine the binding mode of two of the three inhibitor series, and provided a robust system to aid the optimisation of the oxadiazole-substituted benzimidazole inhibitor series. We show that the resulting oxadiazole-substituted aza-benzimidazole is a potent and ligand efficient S6 kinase inhibitor, which blocks the phosphorylation of RPS6 at Ser235/236 in TSC negative HCV29 human bladder cancer cells by inhibiting S6 kinase activity and thus provides a useful tool compound to investigate the function of S6 kinases.


    Organizational Affiliation

    Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA
A
351Bos taurusMutation(s): 5 
Gene Names: PRKACA
EC: 2.7.11.11
Find proteins for P00517 (Bos taurus)
Go to Gene View: PRKACA
Go to UniProtKB:  P00517
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA
I
20Bos taurusMutation(s): 0 
Gene Names: PKIA
Find proteins for Q3SX13 (Bos taurus)
Go to Gene View: PKIA
Go to UniProtKB:  Q3SX13
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Z21
Query on Z21

Download SDF File 
Download CCD File 
A
4-(6-bromo-1-ethyl-1H-imidazo[4,5-c]pyridin-2-yl)-1,2,5-oxadiazol-3-amine
C10 H9 Br N6 O
BDVLCOBTGBLROW-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Z21IC50: 19.7 nM BINDINGMOAD
Z21IC50: 19.7 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.360α = 90.00
b = 75.100β = 90.00
c = 80.270γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
MOSFLMdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2013-11-20
    Type: Database references