3ZRK

Identification of 2-(4-pyridyl)thienopyridinones as GSK-3beta inhibitors

• PDB DOI: https://doi.org/10.2210/pdb3ZRK/pdb

• Classification: TRANSFERASE/PEPTIDE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2011-06-16 Released: 2011-06-29 
• Deposition Author(s): Gentile, G., Bernasconi, G., Pozzan, A., Merlo, G., Marzorati, P., Bamborough, P., Bax, B., Bridges, A., Brough, C., Carter, P., Cutler, G., Neu, M., Takada, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 
  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Identification of 2-(4-Pyridyl)Thienopyridinones as Gsk-3Beta Inhibitors.

Gentile, G., Bernasconi, G., Pozzan, A., Merlo, G., Marzorati, P., Bamborough, P., Bax, B., Bridges, A., Brough, C., Carter, P., Cutler, G., Neu, M., Takada, M.

(2011) Bioorg Med Chem Lett 21: 4823

• PubMed: 21764580 
• DOI: https://doi.org/10.1016/j.bmcl.2011.06.050
• Primary Citation of Related Structures:  
  3ZRK, 3ZRL, 3ZRM


• PubMed Abstract: 
  

  The discovery of a novel series of 2-(4-pyridyl)thienopyridinone GSK-3β inhibitors is reported. X-ray crystallography reveals its binding mode and enables rationalization of the SAR. The initial optimization of the template for improved cellular activity and predicted CNS penetration is also presented.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Neuroscience Centre of Excellence of Drug Discovery, GlaxoSmithKline, Via A Fleming 4, 37135 Verona, Italy. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 92.89 kDa 
• Atom Count: 6,350 
• Modelled Residue Count: 742 
• Deposited Residue Count: 806 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCOGEN SYNTHASE KINASE-3 BETA	A, B	371	Homo sapiens	Mutation(s): 0  EC: 2.7.11.26 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P49841 (Homo sapiens) Explore P49841  Go to UniProtKB:  P49841
PHAROS:  P49841 GTEx:  ENSG00000082701

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTO-ONCOGENE FRAT1	C [auth X], D [auth Y]	32	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q92837 (Homo sapiens) Explore Q92837  Go to UniProtKB:  Q92837
PHAROS:  Q92837 GTEx:  ENSG00000165879

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZRK	I [auth A], O [auth B]	2-(4-PYRIDINYL)FURO[3,2-C]PYRIDIN-4(5H)-ONE C12 H8 N2 O2 NLYCKXUGHPVKMO-UHFFFAOYSA-N
SO4	E [auth A], H [auth A], J [auth B], L [auth B], M [auth B], N [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], G [auth A], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A, B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
ZRK	BindingDB:  3ZRK	IC50: 125.89 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.896	α = 90
b = 151.896	β = 90
c = 201.119	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-29 
Deposition Author(s): Gentile, G., Bernasconi, G., Pozzan, A., Merlo, G., Marzorati, P., Bamborough, P., Bax, B., Bridges, A., Brough, C., Carter, P., Cutler, G., Neu, M., Takada, M.

Revision History  

• Version 1.0: 2011-06-29
  Type: Initial release
  
• Version 1.1: 2012-04-25
  Changes: Database references, Version format compliance
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary