5JTT

Crystal structure of GPb in complex with 8a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Synthetic, enzyme kinetic, and protein crystallographic studies of C-beta-d-glucopyranosyl pyrroles and imidazoles reveal and explain low nanomolar inhibition of human liver glycogen phosphorylase.

Kantsadi, A.L.Bokor, E.Kun, S.Stravodimos, G.A.Chatzileontiadou, D.S.Leonidas, D.D.Juhasz-Toth, E.Szakacs, A.Batta, G.Docsa, T.Gergely, P.Somsak, L.

(2016) Eur.J.Med.Chem. 123: 737-745

  • DOI: 10.1016/j.ejmech.2016.06.049
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • C-β-d-Glucopyranosyl pyrrole derivatives were prepared in the reactions of pyrrole, 2-, and 3-aryl-pyrroles with O-peracetylated β-d-glucopyranosyl trichloroacetimidate, while 2-(β-d-glucopyranosyl) indole was obtained by a cross coupling of O-perben ...

    C-β-d-Glucopyranosyl pyrrole derivatives were prepared in the reactions of pyrrole, 2-, and 3-aryl-pyrroles with O-peracetylated β-d-glucopyranosyl trichloroacetimidate, while 2-(β-d-glucopyranosyl) indole was obtained by a cross coupling of O-perbenzylated β-d-glucopyranosyl acetylene with N-tosyl-2-iodoaniline followed by spontaneous ring closure. An improved synthesis of O-perbenzoylated 2-(β-d-glucopyranosyl) imidazoles was achieved by reacting C-glucopyranosyl formimidates with α-aminoketones. The deprotected compounds were assayed with isoforms of glycogen phosphorylase (GP) to show no activity of the pyrroles against rabbit muscle GPb. The imidazoles proved to be the best known glucose derived inhibitors of not only the muscle enzymes (both a and b) but also of the pharmacologically relevant human liver GPa (Ki = 156 and 26 nM for the 4(5)-phenyl and -(2-naphthyl) derivatives, respectively). An X-ray crystallographic study of the rmGPb-imidazole complexes revealed structural features of the strong binding, and also allowed to explain the absence of inhibition for the pyrrole derivatives.


    Organizational Affiliation

    Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str. 41221, Larissa, Greece. Electronic address: ddleonidas@bio.uth.gr.,Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str. 41221, Larissa, Greece.,Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem tér 1, H-4032, Debrecen, Hungary.,Department of Organic Chemistry, University of Debrecen, POB 400, H-4002, Debrecen, Hungary. Electronic address: somsak.laszlo@science.unideb.hu.,Department of Organic Chemistry, University of Debrecen, POB 400, H-4002, 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
6MY
Query on 6MY

Download SDF File 
Download CCD File 
A
(1S)-1,5-anhydro-1-(5-phenyl-1H-imidazol-2-yl)-D-glucitol
C15 H18 N2 O5
QJGQTBOHSOZKLJ-RKQHYHRCSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-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 %)
6MYKi: 280 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.158 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.600α = 90.00
b = 128.600β = 90.00
c = 116.240γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
REFMACphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2018-01-17
    Type: Data collection