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


View more in-depth experimental data

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