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 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    2PE0, 2PE1

  • 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.


    Related Citations: 
    • 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
    • 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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-phosphoinositide-dependent protein kinase 1A286Homo sapiensMutation(s): 1 
Gene Names: PDPK1PDK1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O15530 (Homo sapiens)
Explore O15530 
Go to UniProtKB:  O15530
PHAROS:  O15530
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
517 (Subject of Investigation/LOI)
Query on 517

Download Ideal Coordinates CCD File 
D [auth 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
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth A], H [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
517 Binding MOAD:  2PE1 IC50: 6 (nM) from 1 assay(s)
PDBBind:  2PE1 IC50: 5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.234α = 90
b = 125.234β = 90
c = 47.696γ = 120
Software Package:
Software NamePurpose
CNXrefinement
XTALVIEWrefinement
X-GENdata reduction
X-GENdata scaling
CNXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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