2PE1

CRYSTAL STRUCTURE OF HUMAN PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 (PDK1) {2-Oxo-3-[1-(1H-pyrrol-2-yl)-eth-(Z)-ylidene]-2,3-dihydro-1H-indol-5-yl}-urea {BX-517} COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Indolinone based phosphoinositide-dependent kinase-1 (PDK1) inhibitors. Part 1: Design, synthesis and biological activity.

Islam, I.Bryant, J.Chou, Y.L.Kochanny, M.J.Lee, W.Phillips, G.B.Yu, H.Adler, M.Whitlow, M.Ho, E.Lentz, D.Polokoff, M.A.Subramanyam, B.Wu, J.M.Zhu, D.Feldman, R.I.Arnaiz, D.O.

(2007) Bioorg.Med.Chem.Lett. 17: 3814-3818

  • DOI: 10.1016/j.bmcl.2007.04.071
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • HTS screening identified 1 with micromolar inhibitory activity against PDK1. Optimization of 1 afforded 4i (BX-517) which has single-digit nanomolar activity against PDK1 and excellent selectivity against PKA.

    HTS screening identified 1 with micromolar inhibitory activity against PDK1. Optimization of 1 afforded 4i (BX-517) which has single-digit nanomolar activity against PDK1 and excellent selectivity against PKA.


    Related Citations: 
    • High Resolution Crystal Structure of the Human Pdk1 Catalytic Domain Defines the Regulatory Phosphopeptide Docking Site.
      Biondi, R.M.,Komander, D.,Thomas, C.C.,Lizcano, J.M.,Deak, M.,Alessi, D.R.,Van Aalten, D.M.F.
      (2002) Embo J. 21: 4219
    • Indolinone based Phhosphoinositide-Dependent Kinase-1 (PDK1) inhibitors- Part 2: Optimization of BX-517
      Islam, I.,Brown, G.,Bryant, J.,Hrvatin, P.,Kochanny, M.J.,Phillips, G.B.,Yuan, S.,Adler, M.,Whitlow, M.,Lentz, D.,Polokoff, M.A.,Wu, J.,Shen, J.,Walters, J.,Ho, E.,Subramanyam, B.,Zhu, D.,Feldman, R.I.,Arnaiz, D.O.
      (2007) TO BE PUBLISHED --: --
    • Novel Small Molecule Inhibitors of 3-Phosphoinositide-Dependent Kinase-1.
      Feldman, R.I.,Wu, J.M.,Polokoff, M.A.,Kochanny, M.J.,Dinter, H.,Zhu, D.,Biroc, S.L.,Alicke, B.,Bryant, J.,Yuan, S.,Buckman, B.O.,Lentz, D.,Ferrer, M.,Whitlow, M.,Adler, M.,Finster, S.,Chang, Z.,Arnaiz, D.O.
      (2005) J.Biol.Chem. 280: 19867


    Organizational Affiliation

    Berlex Biosciences, 2600 Hilltop Dr. Richmond, CA 94804, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-phosphoinositide-dependent protein kinase 1
A
286Homo 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
517
Query on 517

Download SDF File 
Download CCD File 
A
1-{2-OXO-3-[(1R)-1-(1H-PYRROL-2-YL)ETHYL]-2H-INDOL-5-YL}UREA
C15 H14 N4 O2
KJDBLWKTHMHALD-QMMMGPOBSA-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 %)
517IC50: 6 nM BINDINGMOAD
517IC50: 5 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.222 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 125.234α = 90.00
b = 125.234β = 90.00
c = 47.696γ = 120.00
Software Package:
Software NamePurpose
X-GENdata scaling
XTALVIEWrefinement
CNXrefinement
CNXphasing
X-GENdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-04-01 
  • Released Date: 2007-06-12 
  • Deposition Author(s): Whitlow, M., Adler, M.

Revision History 

  • Version 1.0: 2007-06-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance