4C35

PKA-S6K1 Chimera with compound 1 (NU1085) bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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.

(2013) Oncotarget 4: 1647-1661

  • DOI: https://doi.org/10.18632/oncotarget.1255
  • Primary Citation of Related Structures:  
    4C33, 4C34, 4C35, 4C36, 4C37, 4C38

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA351Bos taurusMutation(s): 5 
EC: 2.7.11.11
UniProt
Find proteins for P00517 (Bos taurus)
Explore P00517 
Go to UniProtKB:  P00517
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00517
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHAB [auth I]18Bos taurusMutation(s): 0 
UniProt
Find proteins for Q3SX13 (Bos taurus)
Explore Q3SX13 
Go to UniProtKB:  Q3SX13
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3SX13
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NU3
Query on NU3

Download Ideal Coordinates CCD File 
C [auth A]2-(4-hydroxyphenyl)-1H-benzimidazole-4-carboxamide
C14 H11 N3 O2
KOUGHMOSYJCJLE-UHFFFAOYSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
D [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D 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
Binding Affinity Annotations 
IDSourceBinding Affinity
NU3 PDBBind:  4C35 IC50: 560 (nM) from 1 assay(s)
Binding MOAD:  4C35 IC50: 560 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.44α = 90
b = 73.38β = 90
c = 77.34γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2013-11-20
    Changes: Database references
  • Version 1.2: 2019-10-09
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description