5OX0

Glycogen Phosphorylase in complex with CK898


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 

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Ligand Structure Quality Assessment 


This is version 2.0 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: https://doi.org/10.1016/j.bioorg.2018.02.008
  • Primary Citation of Related Structures:  
    5OWY, 5OWZ, 5OX0, 5OX1, 5OX3, 5OX4

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycogen phosphorylase, muscle form843Oryctolagus cuniculusMutation(s): 0 
EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus)
Explore P00489 
Go to UniProtKB:  P00489
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00489
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B1H
Query on B1H

Download Ideal Coordinates CCD File 
B [auth A](1S)-1,5-anhydro-1-(3-{4-[hydroxy(oxo)azaniumyl]phenyl}-1H-1,2,4-triazol-5-yl)-D-glucitol
C14 H17 N4 O7
UCUAXDZFQJPZOC-RMPHRYRLSA-N
IMP
Query on IMP

Download Ideal Coordinates CCD File 
D [auth A]INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
PLP
Query on PLP

Download Ideal Coordinates CCD File 
C [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Binding Affinity Annotations 
IDSourceBinding Affinity
B1H Binding MOAD:  5OX0 Ki: 3.35e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.55α = 90
b = 128.55β = 90
c = 116.24γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Derived calculations, Structure summary