3QC4

PDK1 in complex with DFG-OUT inhibitor xxx


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

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 1AB314Homo sapiensMutation(s): 2 
Gene Names: PDPK1PDK1
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MP7
Query on MP7

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,BL-PEPTIDE LINKINGC3 H8 N O6 PSER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MP7EC50:  1   nM  BindingDB
MP7IC50 :  2   nM  PDBBind
MP7IC50:  2   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.147α = 90
b = 57.336β = 114.13
c = 83.694γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



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
    Changes: Version format compliance