5HO7

DISCOVERY OF NOVEL 7-AZAINDOLES AS PDK1 INHIBITORS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of novel 7-azaindoles as PDK1 inhibitors.

Wucherer-Plietker, M.Merkul, E.Muller, T.J.Esdar, C.Knochel, T.Heinrich, T.Buchstaller, H.P.Greiner, H.Dorsch, D.Finsinger, D.Calderini, M.Bruge, D.Gradler, U.

(2016) Bioorg Med Chem Lett 26: 3073-3080

  • DOI: 10.1016/j.bmcl.2016.05.005
  • Primary Citation of Related Structures:  
    5HKM, 5HNG, 5HO7, 5HO8

  • PubMed Abstract: 
  • A combined screening strategy using HTS together with focused kinase library and virtual screening led to the identification of diverse chemical series as PDK1 inhibitors. We focused our medicinal chemistry efforts on 7-azaindoles with low micromolar IC50s (e ...

    A combined screening strategy using HTS together with focused kinase library and virtual screening led to the identification of diverse chemical series as PDK1 inhibitors. We focused our medicinal chemistry efforts on 7-azaindoles with low micromolar IC50s (e.g., 16: IC50=1.1μM) in the biochemical PDK1 assay. Our structure-guided optimization efforts considered also PDK1 X-ray structures with weaker binding fragments and resulted in 7-azaindoles with significantly improved biochemical PDK1 potency in the two-digit nanomolar range. However, the most potent analogues only showed moderate activities in a cellular mechanistic assay (42: IC50=2.3μM) together with either low microsomal stability or low permeability. The described structure-activity relationship together with PDK1 X-ray structures and early ADME data provided the basis for our subsequent hit-to-lead program.


    Organizational Affiliation

    Merck KGaA, Biopharma, Global Research & Development, Frankfurter Str. 250, D-64293 Darmstadt, Germany. Electronic address: ulrich.graedler@merckgroup.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-phosphoinositide-dependent protein kinase 1A309Homo sapiensMutation(s): 0 
Gene Names: PDPK1PDK1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O15530 (Homo sapiens)
Explore O15530 
Go to UniProtKB:  O15530
PHAROS:  O15530
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
63L (Subject of Investigation/LOI)
Query on 63L

Download Ideal Coordinates CCD File 
B [auth A]5-amino-3-(methylsulfanyl)-1H-pyrazole-1,4-dicarboxamide
C6 H9 N5 O2 S
TUVCBRIDRHWVLF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
Binding Affinity Annotations 
IDSourceBinding Affinity
63L BindingDB:  5HO7 IC50: 1.70e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.05α = 90
b = 124.05β = 90
c = 47.22γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2016-06-15
    Changes: Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection