3ZDI | pdb_00003zdi

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 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/jm301575n
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 42.44 kDa 
  • Atom Count: 3,029 
  • Modeled Residue Count: 366 
  • Deposited Residue Count: 368 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GLYCOGEN SYNTHASE KINASE-3 BETA350Homo sapiensMutation(s): 0 
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
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
AXIN-118Homo sapiensMutation(s): 0 
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
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / 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
PO4

Query on PO4



Download:Ideal Coordinates CCD File
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Modified Residues  1 Unique
IDChains TypeFormula2D 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 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
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 


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
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary