4AW0 | pdb_00004aw0

Human PDK1 Kinase Domain in Complex with Allosteric Compound PS182 Bound to the PIF-Pocket

• PDB DOI: https://doi.org/10.2210/pdb4AW0/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2012-05-30 Released: 2012-10-03 
• Deposition Author(s): Schulze, J.O., Busschots, K., Lopez-Garcia, L.A., Lammi, C., Stroba, A., Zeuzem, S., Piiper, A., Alzari, P.M., Neimanis, S., Arencibia, J.M., Engel, M., Biondi, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 
  0.188 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Substrate-Selective Inhibition of Protein Kinase Pdk1 by Small Compounds that Bind to the Pif-Pocket Allosteric Docking Site.

Busschots, K., Lopez-Garcia, L.A., Lammi, C., Stroba, A., Zeuzem, S., Piiper, A., Alzari, P.M., Neimanis, S., Arencibia, J.M., Engel, M., Schulze, J.O., Biondi, R.M.

(2012) Chem Biol 19: 1152

• PubMed: 22999883 
• DOI: https://doi.org/10.1016/j.chembiol.2012.07.017
• Primary Citation Related Structures: 
  4AW0, 4AW1


• PubMed Abstract: 
  

  The PIF-pocket of AGC protein kinases participates in the physiologic mechanism of regulation by acting as a docking site for substrates and as a switch for the transduction of the conformational changes needed for activation or inhibition. We describe the effects of compounds that bind to the PIF-pocket of PDK1. In vitro, PS210 is a potent activator of PDK1, and the crystal structure of the PDK1-ATP-PS210 complex shows that PS210 stimulates the closure of the kinase domain. However, in cells, the prodrug of PS210 (PS423) acts as a substrate-selective inhibitor of PDK1, inhibiting the phosphorylation and activation of S6K, which requires docking to the PIF-pocket, but not affecting PKB/Akt. This work describes a tool to study the dynamics of PDK1 activity and a potential approach for drug discovery.

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Organizational Affiliation: 
• Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.6 kDa 
• Atom Count: 2,798 
• Modeled Residue Count: 285 
• Deposited Residue Count: 311 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1	A	311	Homo sapiens	Mutation(s): 2  EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O15530 (Homo sapiens) Explore O15530  Go to UniProtKB:  O15530
PHAROS:  O15530 GTEx:  ENSG00000140992

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	B [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MJF	C [auth A]	[(1R)-3-(4-chlorophenyl)-3-oxo-1-phenylpropyl]propanedioic acid C18 H15 Cl O5 XOOQYQRTMFAOAP-AWEZNQCLSA-N
DTD	G [auth A]	DITHIANE DIOL C4 H8 O2 S2 YPGMOWHXEQDBBV-IMJSIDKUSA-N
DMS	D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free:  0.188 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.27	α = 90
b = 44.01	β = 101.57
c = 47.39	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-03 
Deposition Author(s): Schulze, J.O., Busschots, K., Lopez-Garcia, L.A., Lammi, C., Stroba, A., Zeuzem, S., Piiper, A., Alzari, P.M., Neimanis, S., Arencibia, J.M., Engel, M., Biondi, R.M.

Revision History  

• Version 1.0: 2012-10-03
  Type: Initial release
  
• Version 1.1: 2012-10-10
  Changes: Database references, Derived calculations, Other, Structure summary
• Version 2.0: 2023-12-20
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description
• Version 2.1: 2024-11-13
  Changes: Structure summary