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


Ligand Structure Quality Assessment 


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: https://doi.org/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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-phosphoinositide-dependent protein kinase 1311Homo sapiensMutation(s): 0 
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
GTEx:  ENSG00000140992 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15530
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9BD
Query on 9BD

Download Ideal Coordinates CCD File 
B [auth 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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Binding Affinity Annotations 
IDSourceBinding Affinity
9BD BindingDB:  3H9O IC50: 70 (nM) from 1 assay(s)
PDBBind:  3H9O IC50: 70 (nM) from 1 assay(s)
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



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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