2R7B

Crystal Structure of the Phosphoinositide-dependent Kinase-1 (PDK-1)Catalytic Domain bound to a dibenzonaphthyridine inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Discovery of Dibenzo[c,f][2,7]naphthyridines as Potent and Selective 3-Phosphoinositide-Dependent Kinase-1 Inhibitors.

Gopalsamy, A., Shi, M., Boschelli, D.H., Williamson, R., Olland, A.M., Hu, Y., Krishnamurthy, G., Han, X., Arndt, K., Guo, B.

(2007) J Med Chem 50: 5547-5549

  • DOI: 10.1021/jm070851i
  • Primary Citation of Related Structures:  
    2R7B

  • PubMed Abstract: 

    • With high-throughput screening, substituted dibenzo[c,f][2,7]naphthyridine 1 was identified as a novel potent and selective phosphoinositide-dependent kinase-1 (PDK-1) inhibitor. Various regions of the lead molecule were explored to understand the SA ...

    With high-throughput screening, substituted dibenzo[c,f][2,7]naphthyridine 1 was identified as a novel potent and selective phosphoinositide-dependent kinase-1 (PDK-1) inhibitor. Various regions of the lead molecule were explored to understand the SAR requirement for this scaffold. The crystal structure of 1 with kinase domain of PDK-1 confirmed the binding in the active site. The key interaction of the molecule with the active site residues, observed SAR, and the biological profile are discussed in detail.

    Organizational Affiliation: 

    Chemical and Screening Sciences and Oncology, Wyeth Research, 401 N. Middletown Road, Pearl River, NY 10965, USA. gopalsa@wyeth.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphoinositide-dependent protein kinase 1A312Homo sapiensMutation(s): 0 
Gene Names: PDPK1, PDK1
EC: 2.7.11.1
Find proteins for O15530 (Homo sapiens)
Explore O15530 
Go to UniProtKB:  O15530
NIH Common Fund Data Resources
PHAROS  O15530
GTEx  ENSG00000140992
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
253
Query on 253
Download Ideal Coordinates CCD File 
A
10,11-dimethoxy-4-methyldibenzo[c,f]-2,7-naphthyridine-3,6-diamine
C19 H18 N4 O2
NVINUNQBDNEMSY-UHFFFAOYSA-N		 Ligand Interaction
PSE
Query on PSE
Download Ideal Coordinates CCD File 
A
O-PHOSPHOETHANOLAMINE
C3 H10 N O5 P
WDWYJNPKBKWDBL-GSVOUGTGSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
253IC50:  60   nM  BindingDB
253IC50 :  60   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.225 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.281α = 90
b = 124.281β = 90
c = 47.184γ = 120
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2007-09-07 
  • Released Date: 2008-09-09 
    • Deposition Author(s): Olland, A.M.

Revision History 

  • Version 1.0: 2008-09-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance