3QC4

PDK1 in complex with DFG-OUT inhibitor xxx


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.172 

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, B
314Homo 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
MP7
Query on MP7

Download SDF File 
Download CCD File 
A, B
1-(3,4-difluorobenzyl)-2-oxo-N-{(1R)-2-[(2-oxo-2,3-dihydro-1H-benzimidazol-5-yl)oxy]-1-phenylethyl}-1,2-dihydropyridine-3-carboxamide
C28 H22 F2 N4 O4
GCWCGSPBENFEPE-VWLOTQADSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A, B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MP7EC50: 1 nM (99) BINDINGDB
MP7IC50: 2 nM BINDINGMOAD
MP7IC50: 2 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 183.147α = 90.00
b = 57.336β = 114.13
c = 83.694γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-01-15 
  • Released Date: 2011-04-20 
  • Deposition Author(s): Arndt, J.W.

Revision History 

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