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 
  • R-Value Observed: 0.189 

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
  • Structures With Same Primary Citation

  • 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: 
    • 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 --: --
    • 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
    • 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

    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 1A286Homo sapiensMutation(s): 1 
Gene Names: PDPK1PDK1
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
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
464
Query on 464

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
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 %)
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 
  • R-Value Observed: 0.189 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.223α = 90
b = 123.223β = 90
c = 47.386γ = 120
Software Package:
Software NamePurpose
CNXrefinement
XTALVIEWrefinement
X-GENdata reduction
X-GENdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



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
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance