3PWY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.220 

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-phosphoinositide-dependent protein kinase 1
A
311Homo sapiensMutation(s): 2 
Gene Names: PDPK1 (PDK1)
EC: 2.7.11.1
Find proteins for O15530 (Homo sapiens)
Go to Gene View: PDPK1
Go to UniProtKB:  O15530
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SYP
Query on SYP

Download SDF File 
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: 3.5 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.220 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 122.376α = 90.00
b = 122.376β = 90.00
c = 47.632γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
MOLREPphasing
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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