5OWY

Glycogen Phosphorylase in complex with KS252


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.135 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Probing the beta-pocket of the active site of human liver glycogen phosphorylase with 3-(C-beta-d-glucopyranosyl)-5-(4-substituted-phenyl)-1, 2, 4-triazole inhibitors.

Kyriakis, E.Solovou, T.G.A.Kun, S.Czifrak, K.Szocs, B.Juhasz, L.Bokor, E.Stravodimos, G.A.Kantsadi, A.L.Chatzileontiadou, D.S.M.Skamnaki, V.T.Somsak, L.Leonidas, D.D.

(2018) Bioorg. Chem. 77: 485-493

  • DOI: 10.1016/j.bioorg.2018.02.008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human liver glycogen phosphorylase (hlGP), a key enzyme in glycogen metabolism, is a valid pharmaceutical target for the development of new anti-hyperglycaemic agents for type 2 diabetes. Inhibitor discovery studies have focused on the active site an ...

    Human liver glycogen phosphorylase (hlGP), a key enzyme in glycogen metabolism, is a valid pharmaceutical target for the development of new anti-hyperglycaemic agents for type 2 diabetes. Inhibitor discovery studies have focused on the active site and in particular on glucopyranose based compounds with a β-1 substituent long enough to exploit interactions with a cavity adjacent to the active site, termed the β-pocket. Recently, C-β-d-glucopyranosyl imidazoles and 1, 2, 4-triazoles proved to be the best known glucose derived inhibitors of hlGP. Here we probe the β-pocket by studying the inhibitory effect of six different groups at the para position of 3-(β-d-glucopyranosyl phenyl)-5-phenyl-, 1, 2, 4-triazoles in hlGP by kinetics and X-ray crystallography. The most bioactive compound was the one with an amine substituent to show a K i value of 0.43 μM. Structural studies have revealed the physicochemical diversity of the β-pocket providing information for future rational inhibitor design studies.


    Organizational Affiliation

    Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece.,Department of Organic Chemistry, University of Debrecen, POB 400, H-4002 Debrecen, Hungary.,Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece. Electronic address: ddleonidas@bio.uth.gr.,Department of Organic Chemistry, University of Debrecen, POB 400, H-4002 Debrecen, Hungary. Electronic address: somsak@tigris.unideb.hu.




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
IMP
Query on IMP

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Download CCD File 
A
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
 Ligand Interaction
B0W
Query on B0W

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Download CCD File 
A
4-[5-[(2~{S},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-4~{H}-1,2,4-triazol-3-yl]benzoic acid
C15 H17 N3 O7
UYSDRGPJXJKBOO-RMPHRYRLSA-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: 1.9 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.135 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.460α = 90.00
b = 128.460β = 90.00
c = 116.190γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
REFMACphasing
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release