3QCS

Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 6-[2-Amino-6-(4-morpholinyl)-4-pyrimidinyl]-1H-indazol-3-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.487 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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 inhibi ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-phosphoinositide-dependent protein kinase 1
A
312Homo sapiensMutation(s): 0 
Gene Names: PDPK1 (PDK1)
EC: 2.7.11.1
Find proteins for O15530 (Homo sapiens)
Go to Gene View: PDPK1
Go to UniProtKB:  O15530
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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
3Q1
Query on 3Q1

Download SDF File 
Download CCD File 
A
6-[2-amino-6-(morpholin-4-yl)pyrimidin-4-yl]-2H-indazol-3-amine
C15 H17 N7 O
IBSXLFOFZRSWEZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3Q1IC50: 316 nM (100) BINDINGDB
3Q1IC50: 10 nM BINDINGMOAD
3Q1IC50: 316 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.487 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.174 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 123.848α = 90.00
b = 123.848β = 90.00
c = 47.034γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHENIXrefinement
MAR345dtbdata collection
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2011-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description