6S4H image
Deposition Date 2019-06-28
Release Date 2020-02-19
Last Version Date 2025-04-09
Entry Detail
PDB ID:
6S4H
Keywords:
Title:
The crystal structure of glycogen phosphorylase in complex with 8
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.45 Å
R-Value Free:
0.18
R-Value Work:
0.13
R-Value Observed:
0.13
Space Group:
P 43 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Glycogen phosphorylase, muscle form
Gene (Uniprot):PYGM
Chain IDs:A
Chain Length:843
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Primary Citation
The architecture of hydrogen and sulfur sigma-hole interactions explain differences in the inhibitory potency of C-beta-d-glucopyranosyl thiazoles, imidazoles and an N-beta-d glucopyranosyl tetrazole for human liver glycogen phosphorylase and offer new insights to structure-based design.
Bioorg.Med.Chem. 28 115196 115196 (2020)
PMID: 31767404 DOI: 10.1016/j.bmc.2019.115196

Abstact

C-Glucopyranosyl imidazoles, thiazoles, and an N-glucopyranosyl tetrazole were assessed in vitro and ex vivo for their inhibitory efficiency against isoforms of glycogen phosphorylase (GP; a validated pharmacological target for the development of anti-hyperglycaemic agents). Imidazoles proved to be more potent inhibitors than the corresponding thiazoles or the tetrazole. The most potent derivative has a 2-naphthyl substituent, a Ki value of 3.2 µM for hepatic glycogen phosphorylase, displaying also 60% inhibition of GP activity in HepG2 cells, compared to control vehicle treated cells, at 100 μM. X-Ray crystallography studies of the protein - inhibitor complexes revealed the importance of the architecture of inhibitor associated hydrogen bonds or sulfur σ-hole bond interactions to Asn284 OD1, offering new insights to structure-based design efforts. Moreover, while the 2-glucopyranosyl-tetrazole seems to bind differently from the corresponding 1,2,3-triazole compound, the two inhibitors are equipotent.

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