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 6QA6 | pdb_00006qa6

Glycogen Phosphorylase b in complex with 30


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.199 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.141 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 
    0.144 (Depositor) 

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

Glucopyranosylidene-spiro-imidazolinones, a New Ring System: Synthesis and Evaluation as Glycogen Phosphorylase Inhibitors by Enzyme Kinetics and X-ray Crystallography.

Szabo, K.E., Kyriakis, E., Psarra, A.G., Karra, A.G., Sipos, A., Docsa, T., Stravodimos, G.A., Katsidou, E., Skamnaki, V.T., Liggri, P.G.V., Zographos, S.E., Mandi, A., Kiraly, S.B., Kurtan, T., Leonidas, D.D., Somsak, L.

(2019) J Med Chem 62: 6116-6136

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00356
  • Primary Citation Related Structures: 
    6QA6, 6QA7, 6QA8

  • PubMed Abstract: 

    Epimeric series of aryl-substituted glucopyranosylidene-spiro-imidazolinones, an unprecedented new ring system, were synthesized from the corresponding Schiff bases of O -perbenzoylated (gluculopyranosylamine)onamides by intramolecular ring closure of the aldimine moieties with the carboxamide group elicited by N -bromosuccinimide in pyridine. Test compounds were obtained by Zemplén O -debenzoylation. Stereochemistry and ring tautomers of the new compounds were investigated by NMR, time-dependent density functional theory (TDDFT)-electronic circular dichroism, and DFT-NMR methods. Kinetic studies with rabbit muscle and human liver glycogen phosphorylases showed that the ( R )-imidazolinones were 14-216 times more potent than the ( S ) epimers. The 2-naphthyl-substituted ( R )-imidazolinone was the best inhibitor of the human enzyme ( K i 1.7 μM) and also acted on HepG2 cells (IC 50 177 μM). X-ray crystallography revealed that only the ( R ) epimers bound in the crystal. Their inhibitory efficacy is based on the hydrogen-bonding interactions of the carbonyl oxygen and the NH of the imidazolinone ring.


  • Organizational Affiliation: 
    • Department of Organic Chemistry , University of Debrecen , P.O. Box 400, H-4002 Debrecen , Hungary.

Macromolecule Content 

  • Total Structure Weight: 98.46 kDa 
  • Atom Count: 6,896 
  • Modeled Residue Count: 810 
  • Deposited Residue Count: 843 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycogen phosphorylase, muscle form843Oryctolagus cuniculusMutation(s): 0 
EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus)
Explore P00489 
Go to UniProtKB:  P00489
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00489
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.199 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.141 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 0.144 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.161α = 90
b = 128.161β = 90
c = 115.794γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-24
    Changes: Data collection, Database references
  • Version 1.3: 2025-04-09
    Changes: Data collection, Database references, Structure summary