Novel Isoquinolone PDK1 Inhibitors Discovered through Fragment-Based Lead Discovery

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

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Novel isoquinolone PDK1 inhibitors discovered through fragment-based lead discovery.

Johnson, M.C.Hu, Q.Lingardo, L.Ferre, R.A.Greasley, S.Yan, J.Kath, J.Chen, P.Ermolieff, J.Alton, G.

(2011) J Comput Aided Mol Des 25: 689-698

  • DOI: https://doi.org/10.1007/s10822-011-9456-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Phosphoinositide-dependent kinase-1 (PDK1) is a critical enzyme in the PI3K/AKT pathway and to the activation of AGC family protein kinases, including S6K, SGK, and PKC. Dysregulation of this pathway plays a key role in cancer cell growth, survival and tumor angiogenesis. As such, inhibitors of PDK1 offer the promise of a new therapeutic modality for cancer treatment. Fragment based drug screening has recently become a viable entry point for hit identification. In this work, NMR spectroscopy fragment screening of PDK1 afforded novel chemotypes as orthogonal starting points from HTS screening hits. Compounds identified as hits by NMR spectroscopy were tested in a biochemical assay, and fragments with activity in both assays were clustered. The Pfizer compound file was mined via substructure and 2D similarity search, and the chemotypes were prioritized by ligand efficiency (LE), SAR mining, chemical attractiveness, and chemical enablement of promising vectors. From this effort, an isoquinolone fragment hit, 5 (IC(50) 870 μM, LE = 0.39), was identified as a novel, ligand efficient inhibitor of PDK1 and a suitable scaffold for further optimization. Initially in the absence of crystallographic data, a fragment growing approach efficiently explored four vectors of the isoquinolone scaffold via parallel synthesis to afford a compound with crystallographic data, 16 (IC(50) 41.4 μM, LE = 0.33). Subsequent lead optimization efforts provided 24 (IC(50) 1.8 μM, LE = 0.42), with greater than fivefold selectivity against other key pathway kinases.

  • Organizational Affiliation

    Pfizer Global Research and Development, San Diego, CA 92121, USA, mcjohnson@inchemdesign.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-phosphoinositide-dependent protein kinase 1311Homo sapiensMutation(s): 0 
Gene Names: PDPK1PDK1
UniProt & NIH Common Fund Data Resources
Find proteins for O15530 (Homo sapiens)
Explore O15530 
Go to UniProtKB:  O15530
GTEx:  ENSG00000140992 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15530
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on SEP
Binding Affinity Annotations 
IDSourceBinding Affinity
3S1 PDBBind:  3SC1 IC50: 4.14e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.707α = 90
b = 123.707β = 90
c = 47.295γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
ARPmodel building
WARPmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-26
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Refinement description