3PWY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 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 an ...

    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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-phosphoinositide-dependent protein kinase 1A311Homo sapiensMutation(s): 2 
Gene Names: PDK1PDPK1
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
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SYP
Query on SYP

Download CCD File 
A
N-[2-({6-[(2-sulfanylethyl)amino]pyrimidin-4-yl}amino)ethyl]propanamide
C11 H19 N5 O S
MXLYIGOSAJROJY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance