3NUS

phosphoinositide-dependent kinase-1 (PDK1) with fragment8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Aminoindazole PDK1 Inhibitors: A Case Study in Fragment-Based Drug Discovery.

Medina, J.R.Blackledge, C.W.Heerding, D.A.Campobasso, N.Ward, P.Briand, J.Wright, L.Axten, J.M.

(2010) ACS Med Chem Lett 1: 439-442

  • DOI: 10.1021/ml100136n
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Fragment screening of phosphoinositide-dependent kinase-1 (PDK1) in a biochemical kinase assay afforded hits that were characterized and prioritized based on ligand efficiency and binding interactions with PDK1 as determined by NMR. Subsequent crysta ...

    Fragment screening of phosphoinositide-dependent kinase-1 (PDK1) in a biochemical kinase assay afforded hits that were characterized and prioritized based on ligand efficiency and binding interactions with PDK1 as determined by NMR. Subsequent crystallography and follow-up screening led to the discovery of aminoindazole 19, a potent leadlike PDK1 inhibitor with high ligand efficiency. Well-defined structure-activity relationships and protein crystallography provide a basis for further elaboration and optimization of 19 as a PDK1 inhibitor.


    Organizational Affiliation

    Molecular Discovery Research, Screening and Compound Profiling, GlaxoSmithKline, Research Triangle Park, North Carolina 27709.,Oncology Research, Signal Transduction DPU Medicinal Chemistry.,Molecular Discovery Research, Computational and Structural Chemistry.,Molecular Discovery Research, Analytical Chemistry.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
phosphoinositide-dependent kinase-1
A
286Homo sapiensMutation(s): 0 
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JNZ
Query on JNZ

Download SDF File 
Download CCD File 
A
1H-indazol-3-amine
C7 H7 N3
YDTDKKULPWTHRV-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JNZIC50: 311000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.174 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 123.497α = 90.00
b = 123.497β = 90.00
c = 47.087γ = 120.00
Software Package:
Software NamePurpose
ADSCdata collection
SCALEPACKdata scaling
PHENIXrefinement
PHASERphasing
DENZOdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2018-10-10
    Type: Data collection, Database references, Structure summary