3DU8

Crystal structure of GSK-3 beta in complex with NMS-869553A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

First Cdc7 kinase inhibitors: pyrrolopyridinones as potent and orally active antitumor agents. 2. Lead discovery.

Menichincheri, M.Bargiotti, A.Berthelsen, J.Bertrand, J.A.Bossi, R.Ciavolella, A.Cirla, A.Cristiani, C.Croci, V.D'Alessio, R.Fasolini, M.Fiorentini, F.Forte, B.Isacchi, A.Martina, K.Molinari, A.Montagnoli, A.Orsini, P.Orzi, F.Pesenti, E.Pezzetta, D.Pillan, A.Poggesi, I.Roletto, F.Scolaro, A.Tato, M.Tibolla, M.Valsasina, B.Varasi, M.Volpi, D.Santocanale, C.Vanotti, E.

(2009) J.Med.Chem. 52: 293-307

  • DOI: 10.1021/jm800977q

  • PubMed Abstract: 
  • Cdc7 kinase is a key regulator of the S-phase of the cell cycle, known to promote the activation of DNA replication origins in eukaryotic organisms. Cdc7 inhibition can cause tumor-cell death in a p53-independent manner, supporting the rationale for ...

    Cdc7 kinase is a key regulator of the S-phase of the cell cycle, known to promote the activation of DNA replication origins in eukaryotic organisms. Cdc7 inhibition can cause tumor-cell death in a p53-independent manner, supporting the rationale for developing Cdc7 inhibitors for the treatment of cancer. In this paper, we conclude the structure-activity relationships study of the 2-heteroaryl-pyrrolopyridinone class of compounds that display potent inhibitory activity against Cdc7 kinase. Furthermore, we also describe the discovery of 89S, [(S)-2-(2-aminopyrimidin-4-yl)-7-(2-fluoro-ethyl)-1,5,6,7-tetrahydropyrrolo[3,2-c]pyridin-4-one], as a potent ATP mimetic inhibitor of Cdc7. Compound 89S has a Ki value of 0.5 nM, inhibits cell proliferation of different tumor cell lines with an IC50 in the submicromolar range, and exhibits in vivo tumor growth inhibition of 68% in the A2780 xenograft model.


    Organizational Affiliation

    Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano, Milano, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycogen synthase kinase-3 beta
A, B
422Homo sapiensMutation(s): 0 
Gene Names: GSK3B
EC: 2.7.11.26
Find proteins for P49841 (Homo sapiens)
Go to Gene View: GSK3B
Go to UniProtKB:  P49841
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
553
Query on 553

Download SDF File 
Download CCD File 
A, B
(7S)-2-(2-aminopyrimidin-4-yl)-7-(2-fluoroethyl)-1,5,6,7-tetrahydro-4H-pyrrolo[3,2-c]pyridin-4-one
C13 H14 F N5 O
LCBAQTCTQXHTJG-ZETCQYMHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
553IC50: 146 nM BINDINGMOAD
553IC50: 146 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 82.599α = 90.00
b = 85.810β = 90.00
c = 178.043γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
MxCuBEdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-07-17 
  • Released Date: 2009-03-03 
  • Deposition Author(s): Bossi, R.T.

Revision History 

  • Version 1.0: 2009-03-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description