6GN1

Crystal Structure of Glycogen synthase kinase-3 beta (GSK3B) in Complex with PIK-75


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An Unusual Intramolecular Halogen Bond Guides Conformational Selection.

Tesch, R.Becker, C.Muller, M.P.Beck, M.E.Quambusch, L.Getlik, M.Lategahn, J.Uhlenbrock, N.Costa, F.N.Poleto, M.D.Pinheiro, P.S.M.Rodrigues, D.A.Sant'Anna, C.M.R.Ferreira, F.F.Verli, H.Fraga, C.A.M.Rauh, D.

(2018) Angew. Chem. Int. Ed. Engl. 57: 9970-9975

  • DOI: 10.1002/anie.201804917

  • PubMed Abstract: 
  • PIK-75 is a phosphoinositide-3-kinase (PI3K) α-isoform-selective inhibitor with high potency. Although published structure-activity relationship data show the importance of the NO <sub>2 </sub> and the Br substituents in PIK-75, none of the published ...

    PIK-75 is a phosphoinositide-3-kinase (PI3K) α-isoform-selective inhibitor with high potency. Although published structure-activity relationship data show the importance of the NO 2 and the Br substituents in PIK-75, none of the published studies could correctly determine the underlying reason for their importance. In this publication, we report the first X-ray crystal structure of PIK-75 in complex with the kinase GSK-3β. The structure shows an unusual U-shaped conformation of PIK-75 within the active site of GSK-3β that is likely stabilized by an atypical intramolecular Br⋅⋅⋅NO 2 halogen bond. NMR and MD simulations show that this conformation presumably also exists in solution and leads to a binding-competent preorganization of the PIK-75 molecule, thus explaining its high potency. We therefore suggest that the site-specific incorporation of halogen bonds could be generally used to design conformationally restricted bioactive substances with increased potencies.


    Organizational Affiliation

    Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, CEP, 21941-902, Rio de Janeiro, Brazil.,Departamento de Química, Instituto de Ciências Exatas Universidade Federal Rural do Rio de Janeiro, Seropédica, Brazil.,Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Porto Alegre, Brazil.,Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany.,Bayer AG, division Crop Science, Alfred-Nobel-Strasse 50, 40789, Monheim am Rhein, Germany.,Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Paulo, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycogen synthase kinase-3 beta
B, A
368Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
F4N
Query on F4N

Download SDF File 
Download CCD File 
A, B
~{N}-[(~{E})-(6-bromanylimidazo[1,2-a]pyridin-3-yl)methylideneamino]-~{N},2-dimethyl-5-nitro-benzenesulfonamide
C16 H14 Br N5 O4 S
QTHCAAFKVUWAFI-DJKKODMXSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A, B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 67.630α = 90.00
b = 119.500β = 102.49
c = 67.480γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermanyBMBF 01GS08104
German Federal Ministry for Education and ResearchGermany01ZX1303C

Revision History 

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-08-29
    Type: Data collection, Database references