PDK1 in complex with Compound 8h

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


The identification of 8,9-dimethoxy-5-(2-aminoalkoxy-pyridin-3-yl)-benzo[c][2,7]naphthyridin-4-ylamines as potent inhibitors of 3-phosphoinositide-dependent kinase-1 (PDK-1).

Nittoli, T.Dushin, R.G.Ingalls, C.Cheung, K.Floyd, M.B.Fraser, H.Olland, A.Hu, Y.Grosu, G.Han, X.Arndt, K.Guo, B.Wissner, A.

(2010) Eur J Med Chem 45: 1379-1386

  • DOI: https://doi.org/10.1016/j.ejmech.2009.12.036
  • Primary Citation of Related Structures:  
    3ION, 3IOP

  • PubMed Abstract: 

    A series of 8,9-dimethoxy-5-(2-aminoalkoxy-pyridin-3-yl)-benzo[c][2,7]naphthyridin-4-ylamine-based inhibitors of 3-phosphoinositide-dependent kinase-1 (PDK-1) has been identified. Several examples appear to be potent and relatively selective inhibitors of PDK-1 over the related AGC kinases PKA, PKB/AKT, and p70S6K. The introduction of a stereochemical center beside the amino substituent on the aminoalkoxy-side chain had little effect upon the inhibitory activity against these enzymes, and X-ray crystallographic analyses of a representative pair of enantiomeric inhibitors bound to the active site of PDK-1 revealed comparable binding modes for each enantiomer.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-phosphoinositide-dependent protein kinase 1312Homo sapiensMutation(s): 0 
Gene Names: PDPK1PDK1
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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 8H1

Download Ideal Coordinates CCD File 
B [auth A]2-(5-{[(2S)-2-amino-3-phenylpropyl]oxy}pyridin-3-yl)-8,9-dimethoxybenzo[c][2,7]naphthyridin-4-amine
C28 H27 N5 O3
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
8H1 Binding MOAD:  3ION IC50: 8 (nM) from 1 assay(s)
PDBBind:  3ION IC50: 8 (nM) from 1 assay(s)
BindingDB:  3ION IC50: 8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.368α = 90
b = 123.368β = 90
c = 47.265γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2010-02-09 
  • Deposition Author(s): Olland, A.M.

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations