6GN1

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

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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
  • Primary Citation of Related Structures:  
    6GN1

  • 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 2 and the Br substituents in PIK-75, none of the published studies could correctly determine the underlying reason for their importance ...

    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: 

    Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycogen synthase kinase-3 betaB [auth A],
A [auth B]		368Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49841
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F4N (Subject of Investigation/LOI)
Query on F4N
Download Ideal Coordinates CCD File 
D [auth B],
F [auth A]		~{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
CL
Query on CL
Download Ideal Coordinates CCD File 
C [auth B],
E [auth A]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR		A [auth B],
B [auth A]		L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Binding Affinity Annotations 
IDSourceBinding Affinity
F4N BindingDB:  6GN1 IC50: 10 (nM) from 1 assay(s)
CL BindingDB:  6GN1 EC50: 3.00e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.63α = 90
b = 119.5β = 102.49
c = 67.48γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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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  (Full details and data files)

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