3H9O

Phosphoinositide-dependent protein kinase 1 (PDK-1) in complex with compound 9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Benzo[c][2,7]naphthyridines as inhibitors of PDK-1

Kim, K.H.Wissner, A.Floyd, M.B.Fraser, H.L.Wang, Y.D.Dushin, R.G.Hu, Y.Olland, A.Guo, B.Arndt, K.

(2009) Bioorg Med Chem Lett 19: 5225-5228

  • DOI: 10.1016/j.bmcl.2009.07.007
  • Primary Citation of Related Structures:  
    3H9O

  • PubMed Abstract: 
  • A series of substituted benzo[c][2,7]-naphthyridines were prepared and showed good potency in inhibiting PDK-1. The synthesis and SAR of this series of compounds are presented as well as the X-ray crystal structure of one of these analogs in a comple ...

    A series of substituted benzo[c][2,7]-naphthyridines were prepared and showed good potency in inhibiting PDK-1. The synthesis and SAR of this series of compounds are presented as well as the X-ray crystal structure of one of these analogs in a complex with PDK-1.


    Organizational Affiliation

    Wyeth Research, Chemical Sciences, 401 N. Middletown Road, Pearl River, NY 10965, USA. kimk@wyeth.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-phosphoinositide-dependent protein kinase 1A311Homo sapiensMutation(s): 0 
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9BD
Query on 9BD

Download CCD File 
A
2-(1H-imidazol-1-yl)-9-methoxy-8-(2-methoxyethoxy)benzo[c][2,7]naphthyridin-4-amine
C19 H19 N5 O3
QSSGYSRUMIOURP-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 %)
9BDIC50:  70   nM  BindingDB
9BDIC50 :  70   nM  PDBBind
9BDIC50:  70   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.77α = 90
b = 123.77β = 90
c = 47.116γ = 120
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
AMoREphasing
PHENIXrefinement
SAINTdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-04-30 
  • Released Date: 2009-08-25 
  • Deposition Author(s): Olland, A.M.

Revision History 

  • Version 1.0: 2009-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance