PDBsum entry 6y5c

Transferase

PDB id: 6y5c

Contents

Protein chain

809 a.a.

Ligands

O9T

Waters ×244

PDB id:

6y5c

Name:

Transferase

Title:

The crystal structure of glycogen phosphorylase in complex with 52

Structure:

Glycogen phosphorylase, muscle form. Chain: a. Synonym: myophosphorylase. Ec: 2.4.1.1

Source:

Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986

Resolution:

2.40Å R-factor: 0.170 R-free: 0.211

Authors:

E.Kyriakis,S.M.Koulas,V.T.Skamnaki,D.D.Leonidas

Key ref:

B.A.Chetter et al. (2020). Synthetic flavonoid derivatives targeting the glycogen phosphorylase inhibitor site: QM/MM-PBSA motivated synthesis of substituted 5,7-dihydroxyflavones, crystallography, in vitro kinetics and ex-vivo cellular experiments reveal novel potent inhibitors. Bioorg Chem, 102, 104003. PubMed id: 32771768 DOI: 10.1016/j.bioorg.2020.104003

Date:

25-Feb-20 Release date: 19-Aug-20

Protein chain

P00489  (PYGM_RABIT) -  Glycogen phosphorylase, muscle form from Oryctolagus cuniculus

Seq: 843 a.a.

Struc: 809 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.4.1.1 - glycogen phosphorylase.
• Pathway: Glycogen
• Reaction: [(1->4)-alpha-D-glucosyl](n) + phosphate = [(1->4)-alpha-D-glucosyl](n-1) + alpha-D-glucose 1-phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/j.bioorg.2020.104003

Bioorg Chem 102:104003 (2020)

PubMed id: 32771768

Synthetic flavonoid derivatives targeting the glycogen phosphorylase inhibitor site: QM/MM-PBSA motivated synthesis of substituted 5,7-dihydroxyflavones, crystallography, in vitro kinetics and ex-vivo cellular experiments reveal novel potent inhibitors.

B.A.Chetter, E.Kyriakis, D.Barr, A.G.Karra, E.Katsidou, S.M.Koulas, V.T.Skamnaki, T.J.Snape, A.G.Psarra, D.D.Leonidas, J.M.Hayes.

ABSTRACT

Glycogen phosphorylase (GP) is an important target for the development of new anti-hyperglycaemic agents. Flavonoids are novel inhibitors of GP, but their mode of action is unspecific in terms of the GP binding sites involved. Towards design of synthetic flavonoid analogues acting specifically at the inhibitor site and to exploit the site's hydrophobic pocket, chrysin has been employed as a lead compound for the in silico screening of 1169 new analogues with different B ring substitutions. QM/MM-PBSA binding free energy calculations guided the final selection of eight compounds, subsequently synthesised using a Baker-Venkataraman rearrangement-cyclisation approach. Kinetics experiments against rabbit muscle GPa and GPb together with human liver GPa, revealed three of these compounds (11, 20 and 43) among the most potent that bind at the site (K_i s < 4 µM for all three isoforms), and more potent than previously reported natural flavonoid inhibitors. Multiple inhibition studies revealed binding exclusively at the inhibitor site. The binding is synergistic with glucose suggesting that inhibition could be regulated by blood glucose levels and would decrease as normoglycaemia is achieved. Compound 43 was an effective inhibitor of glycogenolysis in hepatocytes (IC₅₀ = 70 µM), further promoting these compounds for optimization of their drug-like potential. X-ray crystallography studies revealed the B-ring interactions responsible for the observed potencies.