3EBO

Glycogen Phosphorylase b/Chrysin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Sourcing the affinity of flavonoids for the glycogen phosphorylase inhibitor site via crystallography, kinetics and QM/MM-PBSA binding studies: Comparison of chrysin and flavopiridol

Tsitsanou, K.E.Hayes, J.M.Keramioti, M.Mamais, M.Oikonomakos, N.G.Kato, A.Leonidas, D.D.Zographos, S.E.

(2013) Food Chem.Toxicol. 61: 14-27

  • DOI: 10.1016/j.fct.2012.12.030
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Flavonoids have been discovered as novel inhibitors of glycogen phosphorylase (GP), a target to control hyperglycemia in type 2 diabetes. To elucidate the mechanism of inhibition, we have determined the crystal structure of the GPb-chrysin complex at ...

    Flavonoids have been discovered as novel inhibitors of glycogen phosphorylase (GP), a target to control hyperglycemia in type 2 diabetes. To elucidate the mechanism of inhibition, we have determined the crystal structure of the GPb-chrysin complex at 1.9 Å resolution. Chrysin is accommodated at the inhibitor site intercalating between the aromatic side chains of Phe285 and Tyr613 through π-stacking interactions. Chrysin binds to GPb approximately 15 times weaker (Ki=19.01 μM) than flavopiridol (Ki=1.24 μM), exclusively at the inhibitor site, and both inhibitors display similar behavior with respect to AMP. To identify the source of flavopiridols' stronger affinity, molecular docking with Glide and postdocking binding free energy calculations using QM/MM-PBSA have been performed and compared. Whereas docking failed to correctly rank inhibitor binding conformations, the QM/MM-PBSA method employing M06-2X/6-31+G to model the π-stacking interactions correctly reproduced the experimental results. Flavopiridols' greater binding affinity is sourced to favorable interactions of the cationic 4-hydroxypiperidin-1-yl substituent with GPb, with desolvation effects limited by the substituent conformation adopted in the crystallographic complex. Further successful predictions using QM/MM-PBSA for the flavonoid quercetagetin (which binds at the allosteric site) leads us to propose the methodology as a useful and inexpensive tool to predict flavonoid binding.


    Organizational Affiliation

    Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, Athens 11635, Greece.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycogen phosphorylase, muscle form
A
842Oryctolagus 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
57D
Query on 57D

Download SDF File 
Download CCD File 
A
chrysin
5,7-dihydroxy-2-phenyl-4H-chromen-4-one
C15 H10 O4
RTIXKCRFFJGDFG-UHFFFAOYSA-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 %)
57DKi: 19010 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.834α = 90.00
b = 128.834β = 90.00
c = 116.635γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACphasing
REFMACrefinement
DENZOdata reduction
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-01-16
    Type: Database references, Structure summary
  • Version 1.3: 2013-12-11
    Type: Database references
  • Version 1.4: 2018-05-16
    Type: Data collection, Refinement description