Crystal structure of GPb in complex with DK15

Experimental Data Snapshot

  • Resolution: 2.45 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 

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This is version 1.4 of the entry. See complete history


The binding of C5-alkynyl and alkylfurano[2,3-d]pyrimidine glucopyranonucleosides to glycogen phosphorylase b: Synthesis, biochemical and biological assessment.

Kantsadi, A.L.Manta, S.Psarra, A.M.Dimopoulou, A.Kiritsis, C.Parmenopoulou, V.Skamnaki, V.T.Zoumpoulakis, P.Zographos, S.E.Leonidas, D.D.Komiotis, D.

(2012) Eur J Med Chem 54: 740-749

  • DOI: https://doi.org/10.1016/j.ejmech.2012.06.029
  • Primary Citation of Related Structures:  
    4EJ2, 4EKE, 4EKY, 4EL0, 4EL5

  • PubMed Abstract: 

    C5-alkynyl and alkylfurano[2,3-d]pyrimidine glucopyranonucleosides have been synthesized and studied as inhibitors of glycogen phosphorylase b (GPb). Kinetic experiments have shown that most of these compounds were low micromolar inhibitors of the enzyme. The best inhibitor was 1-(β-D-glucopyranosyl)-5-ethynyluracil (K(i)=4.7 μM). Crystallographic analysis of these compounds in complex with GPb revealed that inhibitors with a long C5-alkynyl group exploited interactions with β-pocket of the active site and induced significant conformational changes of the 280s loop compared to GPb in complex with compounds with a short C5-alkynyl group. The results highlight the importance in the length of the aliphatic groups used to enhance inhibitory potency for the exploitation of the hydrophobic β-pocket. The best of the inhibitors had also a moderate effect on glycogenolysis in the cellular lever with an IC(50) value of 291.4 μM.

  • Organizational Affiliation

    Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str. 41221 Larissa, Greece.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycogen phosphorylase, muscle form825Oryctolagus cuniculusMutation(s): 0 
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on D1J

Download Ideal Coordinates CCD File 
B [auth A]1-(beta-D-glucopyranosyl)-5-(pent-1-yn-1-yl)pyrimidine-2,4(1H,3H)-dione
C15 H20 N2 O7
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on LLP
Binding Affinity Annotations 
IDSourceBinding Affinity
D1J PDBBind:  4EKY Ki: 3.03e+5 (nM) from 1 assay(s)
Binding MOAD:  4EKY Ki: 3.03e+5 (nM) from 1 assay(s)
BindingDB:  4EKY Ki: 3.03e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.45 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.674α = 90
b = 128.674β = 90
c = 116.564γ = 90
Software Package:
Software NamePurpose
CrysalisProdata collection
CrysalisProdata 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: 2012-07-25
    Type: Initial release
  • Version 1.1: 2012-08-15
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-12-06
    Changes: Data collection