4EKY

Crystal structure of GPb in complex with DK15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1016/j.ejmech.2012.06.029
  • Primary Citation of Related Structures:  

  • 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 en ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycogen phosphorylase, muscle form
A
825Oryctolagus 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D1J
Query on D1J

Download SDF File 
Download CCD File 
A
1-(beta-D-glucopyranosyl)-5-(pent-1-yn-1-yl)pyrimidine-2,4(1H,3H)-dione
C15 H20 N2 O7
XHEMRIMZCOFGEX-YGEZULPYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
D1JKi: 303000 nM (100) BINDINGDB
D1JKi: 303000 nM BINDINGMOAD
D1JKi: 303000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.161 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.674α = 90.00
b = 128.674β = 90.00
c = 116.564γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
REFMACphasing
CrysalisProdata collection
CrysalisProdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2012-08-15
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description