6QA8

Glycogen Phosphorylase b in complex with 28


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1021/acs.jmedchem.9b00356
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Epimeric series of aryl-substituted glucopyranosylidene-spiro-imidazolinones, an unprecedented new ring system, were synthesized from the corresponding Schiff bases of <i>O </i>-perbenzoylated (gluculopyranosylamine)onamides by intramolecular ring c ...

    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 Medical Chemistry, Faculty of Medicine , University of Debrecen , Egyetem tér 1 , H-4032 Debrecen , Hungary.,Department of Organic Chemistry , University of Debrecen , P.O. Box 400, H-4002 Debrecen , Hungary.,Institute of Biology, Pharmaceutical Chemistry and Biotechnology , National Hellenic Research Foundation , 48 Vassileos Constantinou Avenue , 11635 Athens , Greece.,Department of Biochemistry and Biotechnology , University of Thessaly, Biopolis , 41500 Larissa , Greece.




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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HTE
Query on HTE

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Download CCD File 
A
(5~{S},7~{R},8~{S},9~{S},10~{R})-7-(hydroxymethyl)-8,9,10-tris(oxidanyl)-2-phenyl-6-oxa-1,3-diazaspiro[4.5]dec-1-en-4-one
C14 H16 N2 O6
BCSCGCOVRJYILO-QEGBUVANSA-N
 Ligand Interaction
PLP
Query on PLP

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Download CCD File 
A
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.157 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.233α = 90.00
b = 128.233β = 90.00
c = 116.089γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-10
    Type: Data collection, Database references
  • Version 1.2: 2019-07-24
    Type: Data collection, Database references