8BZS

The crystal structure of glycogen phosphorylase in complex with baicalein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.154 

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Ligand Structure Quality Assessment 


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Literature

Multidisciplinary docking, kinetics and X-ray crystallography studies of baicalein acting as a glycogen phosphorylase inhibitor and determination of its' potential against glioblastoma in cellular models.

Mathomes, R.T.Koulas, S.M.Tsialtas, I.Stravodimos, G.Welsby, P.J.Psarra, A.G.Stasik, I.Leonidas, D.D.Hayes, J.M.

(2023) Chem Biol Interact 382: 110568-110568

  • DOI: https://doi.org/10.1016/j.cbi.2023.110568
  • Primary Citation of Related Structures:  
    8BZS

  • PubMed Abstract: 

    Glycogen phosphorylase (GP) is the rate-determining enzyme in the glycogenolysis pathway. Glioblastoma (GBM) is amongst the most aggressive cancers of the central nervous system. The role of GP and glycogen metabolism in the context of cancer cell metabolic reprogramming is recognised, so that GP inhibitors may have potential treatment benefits. Here, baicalein (5,6,7-trihydroxyflavone) is studied as a GP inhibitor, and for its effects on glycogenolysis and GBM at the cellular level. The compound is revealed as a potent GP inhibitor against human brain GPa (K i  = 32.54 μM), human liver GPa (K i  = 8.77 μM) and rabbit muscle GPb (K i  = 5.66 μM) isoforms. It is also an effective inhibitor of glycogenolysis (IC 50  = 119.6 μM), measured in HepG2 cells. Most significantly, baicalein demonstrated anti-cancer potential through concentration- and time-dependent decrease in cell viability for three GBM cell-lines (U-251 MG, U-87 MG, T98-G) with IC 50 values of ∼20-55 μM (48- and 72-h). Its effectiveness against T98-G suggests potential against GBM with resistance to temozolomide (the first-line therapy) due to a positive O 6 -methylguanine-DNA methyltransferase (MGMT) status. The solved X-ray structure of rabbit muscle GP-baicalein complex will facilitate structure-based design of GP inhibitors. Further exploration of baicalein and other GP inhibitors with different isoform specificities against GBM is suggested.


  • Organizational Affiliation

    School of Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE, United Kingdom.


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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3WL (Subject of Investigation/LOI)
Query on 3WL

Download Ideal Coordinates CCD File 
C [auth A]5,6,7-trihydroxy-2-phenyl-4H-chromen-4-one
C15 H10 O5
FXNFHKRTJBSTCS-UHFFFAOYSA-N
PLP
Query on PLP

Download Ideal Coordinates CCD File 
B [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.154 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.51α = 90
b = 128.51β = 90
c = 116.59γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-13
    Type: Initial release