Crystal Structure of the glycogen phosphorylase B / N-(beta-D-glucopyranosyl)-N'-cyclopropyl oxalamide complex

Experimental Data Snapshot

  • Resolution: 1.93 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.200 

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Binding of oxalyl derivatives of beta-d-glucopyranosylamine to muscle glycogen phosphorylase b.

Hadjiloi, T.Tiraidis, C.Chrysina, E.D.Leonidas, D.D.Oikonomakos, N.G.Tsipos, P.Gimisis, T.

(2006) Bioorg Med Chem 14: 3872-3882

  • DOI: https://doi.org/10.1016/j.bmc.2006.01.045
  • Primary Citation of Related Structures:  
    2F3P, 2F3Q, 2F3S, 2F3U

  • PubMed Abstract: 

    Five oxalyl derivatives of beta-d-glucopyranosylamine were synthesized as potential inhibitors of glycogen phosphorylase (GP). The compounds 1-4 were competitive inhibitors of rabbit muscle GPb (with respect to alpha-d-glucose-1-phosphate) with K(i) values of 0.2-1.4 mM, while compound 5 was not effective up to a concentration of 10 mM. In order to elucidate the structural basis of their inhibition, we analysed the structures of compounds 1-4 in complex with GPb at 1.93-1.96 Angstrom resolution. The complex structures reveal that the inhibitors can be accommodated at the catalytic site at approximately the same position as alpha-d-glucose and stabilize the T-state conformation of the 280 s loop by making several favourable contacts to Asp283 and Asn284 of this loop. Comparison with the lead compound N-acetyl-beta-d-glucopyranosylamine (6) shows that the hydrogen bonding interaction of the amide nitrogen with the main-chain carbonyl oxygen of His377 is not present in these complexes. The differences observed in the K(i) values of the four analogues can be interpreted in terms of subtle conformational changes of protein residues and shifts of water molecules in the vicinity of the catalytic site, variations in van der Waals interactions, conformational entropy and desolvation effects.

  • Organizational Affiliation

    Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48 Vas. Constantinou Ave., 11635 Athens, Greece.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycogen phosphorylase, muscle form842Oryctolagus cuniculusMutation(s): 0 
Gene Names: PYGM
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 8GP

Download Ideal Coordinates CCD File 
C [auth A]N-[(cyclopropylamino)(oxo)acetyl]-beta-D-glucopyranosylamine
C11 H18 N2 O7
Query on PLP

Download Ideal Coordinates CCD File 
C8 H10 N O6 P
Binding Affinity Annotations 
IDSourceBinding Affinity
8GP BindingDB:  2F3U Ki: 1.41e+6 (nM) from 1 assay(s)
Binding MOAD:  2F3U Ki: 1.41e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.93 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.200 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.957α = 90
b = 127.957β = 90
c = 116.03γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-09
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Refinement description, Structure summary