3ZDI

Glycogen Synthase Kinase 3 Beta complexed with Axin Peptide and Inhibitor 7d

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

3,6-Diamino-4-(2-Halophenyl)-2-Benzoylthieno(2,3-B) Pyridine-5-Carbonitriles are Selective Inhibitors of Plasmodium Falciparum Glycogen Synthase Kinase-3 (Pfgsk-3)

Fugel, W., Oberholzer, A.E., Gschloessl, B., Dzikowski, R., Pressburger, N., Preu, L., Pearl, L.H., Baratte, B., Ratin, M., Okun, I., Doerig, C., Kruggel, S., Lemcke, T., Meijer, L., Kunick, C.

(2013) J Med Chem 56: 264

  • DOI: 10.1021/jm301575n
  • Primary Citation of Related Structures:  
    3ZDI

  • PubMed Abstract: 

    • Plasmodium falciparum is the infective agent responsible for malaria tropica. The glycogen synthase kinase-3 of the parasite (PfGSK-3) was suggested as a potential biological target for novel antimalarial drugs. Starting from hit structures identified in a high-throughput screening campaign, 3,6-diamino-4-(2-halophenyl)-2-benzoylthieno[2,3-b]pyridine-5-carbonitriles were discovered as a new class of PfGSK-3 inhibitors ...

    Plasmodium falciparum is the infective agent responsible for malaria tropica. The glycogen synthase kinase-3 of the parasite (PfGSK-3) was suggested as a potential biological target for novel antimalarial drugs. Starting from hit structures identified in a high-throughput screening campaign, 3,6-diamino-4-(2-halophenyl)-2-benzoylthieno[2,3-b]pyridine-5-carbonitriles were discovered as a new class of PfGSK-3 inhibitors. Being less active on GSK-3 homologues of other species, the title compounds showed selectivity in favor of PfGSK-3. Taking into account the X-ray structure of a related molecule in complex with human GSK-3 (HsGSK-3), a model was computed for the comparison of inhibitor complexes with the plasmodial and human enzymes. It was found that subtle differences in the ATP-binding pockets are responsible for the observed PfGSK-3 vs HsGSK-3 selectivity. Representatives of the title compound class exhibited micromolar IC₅₀ values against P. falciparum erythrocyte stage parasites. These results suggest that inhibitors of PfGSK-3 could be developed as potential antimalarial drugs.

    Organizational Affiliation: 

    Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstrasse 55, 38106 Braunschweig, Germany.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLYCOGEN SYNTHASE KINASE-3 BETAA350Homo sapiensMutation(s): 0 
Gene Names: GSK3B
EC: 2.7.11.26 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P49841 (Homo sapiens)
Explore P49841 
Go to UniProtKB:  P49841
PHAROS:  P49841
GTEx:  ENSG00000082701 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49841
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
AXIN-1B18Homo sapiensMutation(s): 0 
Gene Names: AXIN1, AXIN
UniProt & NIH Common Fund Data Resources
Find proteins for O15169 (Homo sapiens)
Explore O15169 
Go to UniProtKB:  O15169
PHAROS:  O15169
GTEx:  ENSG00000103126 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15169
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UGJ
Query on UGJ
Download Ideal Coordinates CCD File 
D [auth A]3,6-Diamino-4-(2-chlorophenyl)thieno[2,3-b]pyridine-2,5-dicarbonitrile
C15 H8 Cl N5 S
ZYCDWPCMXHYGRS-UHFFFAOYSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR		A L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.147α = 90
b = 76.157β = 90
c = 86.545γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-01-30
    Changes: Database references