3QD3

Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 1,1-Dimethylethyl {(3R,6S)-1-[2-amino-6-(3-amino-1H-indazol-6-yl)-4-pyrimidinyl]-6-methyl-3-piperidinyl}carbamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-Based Design of Potent and Selective 3-Phosphoinositide-Dependent Kinase-1 (PDK1) Inhibitors.

Medina, J.R.Becker, C.J.Blackledge, C.W.Duquenne, C.Feng, Y.Grant, S.W.Heerding, D.Li, W.H.Miller, W.H.Romeril, S.P.Scherzer, D.Shu, A.Bobko, M.A.Chadderton, A.R.Dumble, M.Gardiner, C.M.Gilbert, S.Liu, Q.Rabindran, S.K.Sudakin, V.Xiang, H.Brady, P.G.Campobasso, N.Ward, P.Axten, J.M.

(2011) J Med Chem 54: 1871-1895

  • DOI: 10.1021/jm101527u
  • Primary Citation of Related Structures:  
    3QCX, 3QCY, 3QD0, 3QCQ, 3QD3, 3QCS, 3QD4

  • PubMed Abstract: 
  • Phosphoinositide-dependent protein kinase-1(PDK1) is a master regulator of the AGC family of kinases and an integral component of the PI3K/AKT/mTOR pathway. As this pathway is among the most commonly deregulated across all cancers, a selective inhibitor of PDK1 might have utility as an anticancer agent ...

    Phosphoinositide-dependent protein kinase-1(PDK1) is a master regulator of the AGC family of kinases and an integral component of the PI3K/AKT/mTOR pathway. As this pathway is among the most commonly deregulated across all cancers, a selective inhibitor of PDK1 might have utility as an anticancer agent. Herein we describe our lead optimization of compound 1 toward highly potent and selective PDK1 inhibitors via a structure-based design strategy. The most potent and selective inhibitors demonstrated submicromolar activity as measured by inhibition of phosphorylation of PDK1 substrates as well as antiproliferative activity against a subset of AML cell lines. In addition, reduction of phosphorylation of PDK1 substrates was demonstrated in vivo in mice bearing OCl-AML2 xenografts. These observations demonstrate the utility of these molecules as tools to further delineate the biology of PDK1 and the potential pharmacological uses of a PDK1 inhibitor.


    Related Citations: 
    • Aminoindazole PDK1 Inhibitors: A Case Study in Fragment-Based Drug Discovery
      Medina, J.R., Blackledge, C.W., Heerding, D.A., Campobasso, N., Ward, P., Briand, J., Wright, L., Axten, J.M.
      (2010) ACS Med Chem Lett 1: 439

    Organizational Affiliation

    Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States. jesus.r.medina@gsk.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-phosphoinositide-dependent protein kinase 1A312Homo sapiensMutation(s): 0 
Gene Names: PDK1PDPK1
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
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3Q5
Query on 3Q5

Download CCD File 
A
tert-butyl {(3R,6S)-1-[2-amino-6-(3-amino-2H-indazol-6-yl)pyrimidin-4-yl]-6-methylpiperidin-3-yl}carbamate
C22 H30 N8 O2
GAMJJHMLLXIWRZ-GXTWGEPZSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3Q5IC50:  10   nM  Binding MOAD
3Q5IC50:  10   nM  BindingDB
3Q5IC50 :  10   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.533α = 90
b = 123.533β = 90
c = 46.87γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2011-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance