4RRV

Crystal structure of PDK1 in complex with ATP and PIFtide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.412 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.134 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A small-molecule mimic of a peptide docking motif inhibits the protein kinase PDK1.

Rettenmaier, T.J.Sadowsky, J.D.Thomsen, N.D.Chen, S.C.Doak, A.K.Arkin, M.R.Wells, J.A.

(2014) Proc.Natl.Acad.Sci.USA 111: 18590-18595

  • DOI: 10.1073/pnas.1415365112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • There is great interest in developing selective protein kinase inhibitors by targeting allosteric sites, but these sites often involve protein-protein or protein-peptide interfaces that are very challenging to target with small molecules. Here we pre ...

    There is great interest in developing selective protein kinase inhibitors by targeting allosteric sites, but these sites often involve protein-protein or protein-peptide interfaces that are very challenging to target with small molecules. Here we present a systematic approach to targeting a functionally conserved allosteric site on the protein kinase PDK1 called the PDK1-interacting fragment (PIF)tide-binding site, or PIF pocket. More than two dozen prosurvival and progrowth kinases dock a conserved peptide tail into this binding site, which recruits them to PDK1 to become activated. Using a site-directed chemical screen, we identified and chemically optimized ligand-efficient, selective, and cell-penetrant small molecules (molecular weight ∼ 380 Da) that compete with the peptide docking motif for binding to PDK1. We solved the first high-resolution structure of a peptide docking motif (PIFtide) bound to PDK1 and mapped binding energy hot spots using mutational analysis. We then solved structures of PDK1 bound to the allosteric small molecules, which revealed a binding mode that remarkably mimics three of five hot-spot residues in PIFtide. These allosteric small molecules are substrate-selective PDK1 inhibitors when used as single agents, but when combined with an ATP-competitive inhibitor, they completely suppress the activation of the downstream kinases. This work provides a promising new scaffold for the development of high-affinity PIF pocket ligands, which may be used to enhance the anticancer activity of existing PDK1 inhibitors. Moreover, our results provide further impetus for exploring the helix αC patches of other protein kinases as potential therapeutic targets even though they involve protein-protein interfaces.


    Organizational Affiliation

    Chemistry and Chemical Biology Graduate Program, Department of Pharmaceutical Chemistry.,Department of Pharmaceutical Chemistry, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158 jim.wells@ucsf.edu.,Department of Pharmaceutical Chemistry.,Small Molecule Discovery Center, and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-phosphoinositide-dependent protein kinase 1
A
311Homo sapiensMutation(s): 2 
Gene Names: PDPK1 (PDK1)
EC: 2.7.11.1
Find proteins for O15530 (Homo sapiens)
Go to Gene View: PDPK1
Go to UniProtKB:  O15530
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase N2
B
15Homo sapiensMutation(s): 0 
Gene Names: PKN2 (PRK2, PRKCL2)
EC: 2.7.11.13
Find proteins for Q16513 (Homo sapiens)
Go to Gene View: PKN2
Go to UniProtKB:  Q16513
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.412 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.134 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 148.973α = 90.00
b = 44.536β = 101.40
c = 47.799γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHENIXrefinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-17
    Type: Initial release
  • Version 1.1: 2015-01-14
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description