6F3S

The crystal structure of Glycogen Phosphorylase in complex with 10d


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.135 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A multidisciplinary study of 3-( beta-d-glucopyranosyl)-5-substituted-1,2,4-triazole derivatives as glycogen phosphorylase inhibitors: Computation, synthesis, crystallography and kinetics reveal new potent inhibitors.

Kun, S.Begum, J.Kyriakis, E.Stamati, E.C.V.Barkas, T.A.Szennyes, E.Bokor, E.Szabo, K.E.Stravodimos, G.A.Sipos, A.Docsa, T.Gergely, P.Moffatt, C.Patraskaki, M.S.Kokolaki, M.C.Gkerdi, A.Skamnaki, V.T.Leonidas, D.D.Somsak, L.Hayes, J.M.

(2018) Eur J Med Chem 147: 266-278

  • DOI: 10.1016/j.ejmech.2018.01.095
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 3-(β-d-Glucopyranosyl)-5-substituted-1,2,4-triazoles have been revealed as an effective scaffold for the development of potent glycogen phosphorylase (GP) inhibitors but with the potency very sensitive to the nature of the alkyl/aryl 5-substituent (K ...

    3-(β-d-Glucopyranosyl)-5-substituted-1,2,4-triazoles have been revealed as an effective scaffold for the development of potent glycogen phosphorylase (GP) inhibitors but with the potency very sensitive to the nature of the alkyl/aryl 5-substituent (Kun et al., Eur. J. Med. Chem. 2014, 76, 567). For a training set of these ligands, quantum mechanics-polarized ligand docking (QM-PLD) demonstrated good potential to identify larger differences in potencies (predictive index PI = 0.82) and potent inhibitors with K i 's < 10 μM (AU-ROC = 0.86). Accordingly, in silico screening of 2335 new analogues exploiting the ZINC docking database was performed and nine predicted candidates selected for synthesis. The compounds were prepared in O-perbenzoylated forms by either ring transformation of 5-β-d-glucopyranosyl tetrazole by N-benzyl-arenecarboximidoyl chlorides, ring closure of C-(β-d-glucopyranosyl)formamidrazone with aroyl chlorides, or that of N-(β-d-glucopyranosylcarbonyl)arenethiocarboxamides by hydrazine, followed by deprotections. Kinetics experiments against rabbit muscle GPb (rmGPb) and human liver GPa (hlGPa) revealed five compounds as potent low μM inhibitors with three of these on the submicromolar range for rmGPa. X-ray crystallographic analysis sourced the potency to a combination of favorable interactions from the 1,2,4-triazole and suitable aryl substituents in the GP catalytic site. The compounds also revealed promising calculated pharmacokinetic profiles.


    Organizational Affiliation

    Department of Biochemistry & Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece.,Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary.,School of Physical Sciences & Computing, Division of Chemistry, University of Central Lancashire, Preston PR1 2HE, United Kingdom; School of Chemistry, University of Leeds, Leeds, LS2 9JT, United Kingdom.,Department of Organic Chemistry, University of Debrecen, POB 400, H-4002 Debrecen, Hungary.,School of Physical Sciences & Computing, Division of Chemistry, University of Central Lancashire, Preston PR1 2HE, United Kingdom. Electronic address: jhayes@uclan.ac.uk.,Department of Biochemistry & Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece. Electronic address: ddleonidas@bio.uth.gr.,Health and Life Sciences, De Montfort University, Gateway House, Leicester, LE1 9BH, United Kingdom.,Department of Organic Chemistry, University of Debrecen, POB 400, H-4002 Debrecen, Hungary. Electronic address: somsak.laszlo@science.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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
CKW
Query on CKW

Download SDF File 
Download CCD File 
A
(2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-[5-(4-phenylphenyl)-4~{H}-1,2,4-triazol-3-yl]oxane-3,4,5-triol
C20 H21 N3 O5
NIARDQNUDKGRGO-UYTYNIKBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.135 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.763α = 90.00
b = 128.763β = 90.00
c = 116.391γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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