Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43542.37 
• Atom Count: 2960 
• Residue Count: 371 
• Unique protein chains: 2

4C36

PKA-S6K1 Chimera with compound 15e (CCT147581) bound

• DOI: 10.2210/pdb4C36/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Bos taurus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 5 


• Deposited: 2013-08-21 Released: 2013-10-09 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.190 
• R-Value Work: 0.157 

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

• PubMed: 24072592 
• DOI: 10.18632/oncotarget.1255
• Primary Citation of Related Structures:  
  4C38, 4C37, 4C35, 4C34, 4C33


• 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA	A	351	Bos taurus	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA	I	20	Bos taurus	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZO9	A	4-[1-(cyclopropylmethyl)-1H-benzimidazol-2-yl]-1,2,5-oxadiazol-3-amine C13 H13 N5 O LLDVRUBUBPSOMY-UHFFFAOYSA-N
MOH	I	METHANOL C H4 O OKKJLVBELUTLKV-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ZO9	Ki: 380 nM (98) BINDINGDB
ZO9	IC50: 19.8 nM BINDINGMOAD
ZO9	IC50: 19.8 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.190 
• R-Value Work: 0.157 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 72.560	α = 90.00
b = 75.850	β = 90.00
c = 80.380	γ = 90.00

Software Package:

Software Name	Purpose
MOSFLM	data reduction
PHASER	phasing
BUSTER	refinement
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-08-21 
• Released Date: 2013-10-09 
• Deposition Author(s): 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.

Revision History 

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