Crystal structure of an extender (SPD28345)-modified human PDK1 complex 2

Experimental Data Snapshot

  • Resolution: 3.50 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.226 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Discovery of a potent and highly selective PDK1 inhibitor via fragment-based drug discovery.

Erlanson, D.A.Arndt, J.W.Cancilla, M.T.Cao, K.Elling, R.A.English, N.Friedman, J.Hansen, S.K.Hession, C.Joseph, I.Kumaravel, G.Lee, W.C.Lind, K.E.McDowell, R.S.Miatkowski, K.Nguyen, C.Nguyen, T.B.Park, S.Pathan, N.Penny, D.M.Romanowski, M.J.Scott, D.Silvian, L.Simmons, R.L.Tangonan, B.T.Yang, W.Sun, L.

(2011) Bioorg Med Chem Lett 21: 3078-3083

  • DOI: https://doi.org/10.1016/j.bmcl.2011.03.032
  • Primary Citation of Related Structures:  
    3PWY, 3QC4

  • PubMed Abstract: 

    We report the use of a fragment-based lead discovery method, Tethering with extenders, to discover a pyridinone fragment that binds in an adaptive site of the protein PDK1. With subsequent medicinal chemistry, this led to the discovery of a potent and highly selective inhibitor of PDK1, which binds in the 'DFG-out' conformation.

  • Organizational Affiliation

    Sunesis Pharmaceuticals, Inc., 395 Oyster Point Blvd., South San Francisco, CA 94080, USA. derlanson@carmot.us

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-phosphoinositide-dependent protein kinase 1311Homo sapiensMutation(s): 2 
Gene Names: PDK1PDPK1
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
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SYP

Download Ideal Coordinates CCD File 
B [auth A]N-[2-({6-[(2-sulfanylethyl)amino]pyrimidin-4-yl}amino)ethyl]propanamide
C11 H19 N5 O S
Experimental Data & Validation

Experimental Data

  • Resolution: 3.50 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.226 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.376α = 90
b = 122.376β = 90
c = 47.632γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata 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: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description