Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 43.54 kDa 
• Atom Count: 3337 
• Modelled Residue Count: 358 
• Deposited Residue Count: 371 
• Unique protein chains: 2

4C36

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

• PDB DOI: 10.2210/pdb4C36/pdb

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


• 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 
• R-Value Observed: 0.158 

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:  
  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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA	A	351	Bos taurus	Mutation(s): 5  Gene Names: PRKACA EC: 2.7.11.11
UniProt
Find proteins for P00517 (Bos taurus) Explore P00517  Go to UniProtKB:  P00517

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA	B [auth I]	20	Bos taurus	Mutation(s): 0  Gene Names: PKIA
UniProt
Find proteins for Q3SX13 (Bos taurus) Explore Q3SX13  Go to UniProtKB:  Q3SX13

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZO9	C [auth A]	4-[1-(cyclopropylmethyl)-1H-benzimidazol-2-yl]-1,2,5-oxadiazol-3-amine C13 H13 N5 O LLDVRUBUBPSOMY-UHFFFAOYSA-N
MOH	D [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
ZO9	BindingDB:  4C36	Ki: 380 (nM) from 1 assay(s)
	PDBBind:  4C36	IC50: 19.8 (nM) from 1 assay(s)
	Binding MOAD:  4C36	IC50: 19.8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.190 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.56	α = 90
b = 75.85	β = 90
c = 80.38	γ = 90

Software Package:

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

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
  Changes: Database references
• Version 1.2: 2019-10-09
  Changes: Data collection, Database references, Derived calculations, Other