2PE2

CRYSTAL STRUCTURE OF HUMAN PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 (PDK1) 3-{5-[2-Oxo-5-ureido-1,2-dihydro-indol-(3Z)-ylidenemethyl]-1H-pyrrol-3-yl}-N-(2-piperidin-1-yl-ethyl)-benzamide COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.188 

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 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) Bioorg.Med.Chem.Lett. 17: 3819-3825

  • DOI: 10.1016/j.bmcl.2007.05.060

  • PubMed Abstract: 
  • Based on the lead compound BX-517, a series of C-4' substituted indolinones have been synthesized and evaluated for PDK1 inhibition. Modification at C-4' of the pyrrole afforded potent compounds (7b and 7d) with improved solubility and ADME propertie ...

    Based on the lead compound BX-517, a series of C-4' substituted indolinones have been synthesized and evaluated for PDK1 inhibition. Modification at C-4' of the pyrrole afforded potent compounds (7b and 7d) with improved solubility and ADME properties. In this letter, we describe the synthesis, selectivity profile, and pharmacokinetic data of selected compounds.


    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
    • 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
    • Indolinone based Phhosphoinositide-Dependent Kinase-1 (PDK1) inhibitors- Part 1: Design, Synthesis and Billogical 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) TO BE PUBLISHED --: --


    Organizational Affiliation

    Berlex Biosciences, 2600 Hilltop Dr. Richmond, CA 94804, USA. imadulislam@yahoo.com




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
464
Query on 464

Download SDF File 
Download CCD File 
A
3-[5-({5-[(AMINOCARBONYL)AMINO]-2-OXO-2H-INDOL-3-YL}METHYL)-1H-PYRROL-3-YL]-N-(2-PIPERIDIN-1-YLETHYL)BENZAMIDE
C28 H30 N6 O3
PWZOBKJHPWISGC-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 %)
464IC50: 4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.188 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 123.223α = 90.00
b = 123.223β = 90.00
c = 47.386γ = 120.00
Software Package:
Software NamePurpose
XTALVIEWrefinement
X-GENdata scaling
X-PLORphasing
CNXrefinement
X-GENdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-04-01 
  • Released Date: 2007-06-19 
  • Deposition Author(s): Whitlow, M., Adler, M.

Revision History 

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance