3NAX

PDK1 in complex with inhibitor MP7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Genetic and pharmacological inhibition of PDK1 in cancer cells: characterization of a selective allosteric kinase inhibitor.

Nagashima, K.Shumway, S.D.Sathyanarayanan, S.Chen, A.H.Dolinski, B.Xu, Y.Keilhack, H.Nguyen, T.Wiznerowicz, M.Li, L.Lutterbach, B.A.Chi, A.Paweletz, C.Allison, T.Yan, Y.Munshi, S.K.Klippel, A.Kraus, M.Bobkova, E.V.Deshmukh, S.Xu, Z.Mueller, U.Szewczak, A.A.Pan, B.S.Richon, V.Pollock, R.Blume-Jensen, P.Northrup, A.Andersen, J.N.

(2011) J Biol Chem 286: 6433-6448

  • DOI: 10.1074/jbc.M110.156463
  • Primary Citation of Related Structures:  
    3NAX

  • PubMed Abstract: 
  • Phosphoinositide-dependent kinase 1 (PDK1) is a critical activator of multiple prosurvival and oncogenic protein kinases and has garnered considerable interest as an oncology drug target. Despite progress characterizing PDK1 as a therapeutic target, ...

    Phosphoinositide-dependent kinase 1 (PDK1) is a critical activator of multiple prosurvival and oncogenic protein kinases and has garnered considerable interest as an oncology drug target. Despite progress characterizing PDK1 as a therapeutic target, pharmacological support is lacking due to the prevalence of nonspecific inhibitors. Here, we benchmark literature and newly developed inhibitors and conduct parallel genetic and pharmacological queries into PDK1 function in cancer cells. Through kinase selectivity profiling and x-ray crystallographic studies, we identify an exquisitely selective PDK1 inhibitor (compound 7) that uniquely binds to the inactive kinase conformation (DFG-out). In contrast to compounds 1-5, which are classical ATP-competitive kinase inhibitors (DFG-in), compound 7 specifically inhibits cellular PDK1 T-loop phosphorylation (Ser-241), supporting its unique binding mode. Interfering with PDK1 activity has minimal antiproliferative effect on cells growing as plastic-attached monolayer cultures (i.e. standard tissue culture conditions) despite reduced phosphorylation of AKT, RSK, and S6RP. However, selective PDK1 inhibition impairs anchorage-independent growth, invasion, and cancer cell migration. Compound 7 inhibits colony formation in a subset of cancer cell lines (four of 10) and primary xenograft tumor lines (nine of 57). RNAi-mediated knockdown corroborates the PDK1 dependence in cell lines and identifies candidate biomarkers of drug response. In summary, our profiling studies define a uniquely selective and cell-potent PDK1 inhibitor, and the convergence of genetic and pharmacological phenotypes supports a role of PDK1 in tumorigenesis in the context of three-dimensional in vitro culture systems.


    Organizational Affiliation

    Merck Research Laboratories, Boston, Massachusetts 02115, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-phosphoinositide-dependent protein kinase 1A311Homo sapiensMutation(s): 0 
Gene Names: PDPK1PDK1
EC: 2.7.11.1
Find proteins for O15530 (Homo sapiens)
Explore O15530 
Go to UniProtKB:  O15530
NIH Common Fund Data Resources
PHAROS  O15530
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MP7
Query on MP7

Download CCD File 
A
1-(3,4-difluorobenzyl)-2-oxo-N-{(1R)-2-[(2-oxo-2,3-dihydro-1H-benzimidazol-5-yl)oxy]-1-phenylethyl}-1,2-dihydropyridine-3-carboxamide
C28 H22 F2 N4 O4
GCWCGSPBENFEPE-VWLOTQADSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MP7EC50:  1   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.668α = 109.27
b = 44.943β = 90.5
c = 42.204γ = 62.43
Software Package:
Software NamePurpose
StructureStudiodata collection
AMoREphasing
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance