4CTM

Glucopyranosylidene-spiro-iminothiazolidinone, a New Bicyclic Ring System: Synthesis, Derivatization, and Evaluation as Glycogen Phosphorylase Inhibitors by Enzyme Kinetic and Crystallographic Methods


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Glucopyranosylidene-Spiro-Iminothiazolidinone, a New Bicyclic Ring System: Synthesis, Derivatization, and Evaluation for Inhibition of Glycogen Phosphorylase by Enzyme Kinetic and Crystallographic Methods.

Czifrak, K.Deak, S.Pahi, A.Kover, K.E.Docsa, T.Gergely, P.Alexacou, K.M.Papakonstantinou, M.Leonidas, D.D.Zographos, S.E.Chrysina, E.D.Somsak, L.

(2014) Bioorg.Med.Chem. 22: 4028

  • DOI: 10.1016/j.bmc.2014.05.076
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The reaction of thiourea with O-perbenzoylated C-(1-bromo-1-deoxy-β-D-glucopyranosyl)formamide gave the new anomeric spirocycle 1R-1,5-anhydro-D-glucitol-spiro-[1,5]-2-imino-1,3-thiazolidin-4-one. Acylation and sulfonylation with the corresponding ac ...

    The reaction of thiourea with O-perbenzoylated C-(1-bromo-1-deoxy-β-D-glucopyranosyl)formamide gave the new anomeric spirocycle 1R-1,5-anhydro-D-glucitol-spiro-[1,5]-2-imino-1,3-thiazolidin-4-one. Acylation and sulfonylation with the corresponding acyl chlorides (RCOCl or RSO₂Cl where R=tBu, Ph, 4-Me-C₆H₄, 1- and 2-naphthyl) produced the corresponding 2-acylimino- and 2-sulfonylimino-thiazolidinones, respectively. Alkylation by MeI, allyl-bromide and BnBr produced mixtures of the respective N-alkylimino- and N,N'-dialkyl-imino-thiazolidinones, while reactions with 1,2-dibromoethane and 1,3-dibromopropane furnished spirocyclic 5,6-dihydro-imidazo[2,1-b]thiazolidin-3-one and 6,7-dihydro-5H-thiazolidino[3,2-a]pyrimidin-3-one, respectively. Removal of the O-benzoyl protecting groups by the Zemplén protocol led to test compounds most of which proved micromolar inhibitors of rabbit muscle glycogen phosphorylase b (RMGPb). Best inhibitors were the 2-benzoylimino- (Ki=9μM) and the 2-naphthoylimino-thiazolidinones (Ki=10 μM). Crystallographic studies of the unsubstituted spiro-thiazolidinone and the above most efficient inhibitors in complex with RMGPb confirmed the preference and inhibitory effect that aromatic (and especially 2-naphthyl) derivatives show for the catalytic site promoting the inactive conformation of the enzyme.


    Related Citations: 
    • The Structure of a Glycogen Phosphorylase Glucopyranose Spirohydantoin Complex at 1.8 A Resolution and 100 K: The Role of the Water Structure and its Contribution to Binding.
      Gregoriou, M.,Noble, M.E.,Watson, K.A.,Garman, E.F.,Krulle, T.M.,De La Fuente, C.,Fleet, G.W.,Oikonomakos, N.G.,Johnson, L.N.
      (1998) Protein Sci. 7: 915


    Organizational Affiliation

    Department of Organic Chemistry, University of Debrecen, POB 20, H-4010 Debrecen, Hungary.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCOGEN PHOSPHORYLASE, MUSCLE FORM
A
843Oryctolagus cuniculusMutation(s): 0 
Gene Names: PYGM
EC: 2.4.1.1
Find proteins for P00489 (Oryctolagus cuniculus)
Go to Gene View: PYGM
Go to UniProtKB:  P00489
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MIF
Query on MIF

Download SDF File 
Download CCD File 
A
(5R,7R,8S,9S,10R)-8,9,10-trihydroxy-7-(hydroxymethyl)-2-imino-6-oxa-1-thia-3-azaspiro[4.5]decan-4-one
C8 H12 N2 O6 S
UADFNVXVJZELQM-UXDJRKLDSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MIFKi: 24000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.173 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.240α = 90.00
b = 128.240β = 90.00
c = 115.900γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-06
    Type: Initial release