1WW3

Crystallographic studies on two bioisosteric analogues, N-acetyl-beta-D-glucopyranosylamine and N-trifluoroacetyl-beta-D-glucopyranosylamine, potent inhibitors of muscle glycogen phosphorylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystallographic studies on two bioisosteric analogues, N-acetyl-beta-d-glucopyranosylamine and N-trifluoroacetyl-beta-d-glucopyranosylamine, potent inhibitors of muscle glycogen phosphorylase

Anagnostou, E.Kosmopoulou, M.N.Chrysina, E.D.Leonidas, D.D.Hadjiloi, T.Tiraidis, C.Zographos, S.E.Gyorgydeak, Z.Somsak, L.Docsa, T.Gergely, P.Kolisis, F.N.Oikonomakos, N.G.

(2006) Bioorg Med Chem 14: 181-189

  • DOI: 10.1016/j.bmc.2005.08.010
  • Primary Citation of Related Structures:  
    1WW3, 1WW2

  • PubMed Abstract: 
  • Structure-based inhibitor design has led to the discovery of a number of potent inhibitors of glycogen phosphorylase b (GPb), N-acyl derivatives of beta-D-glucopyranosylamine, that bind at the catalytic site of the enzyme. The first good inhibitor in this class of compounds, N-acetyl-beta-D-glucopyranosylamine (NAG) (K(i) = 32 microM), has been previously characterized by biochemical, biological and crystallographic experiments at 2 ...

    Structure-based inhibitor design has led to the discovery of a number of potent inhibitors of glycogen phosphorylase b (GPb), N-acyl derivatives of beta-D-glucopyranosylamine, that bind at the catalytic site of the enzyme. The first good inhibitor in this class of compounds, N-acetyl-beta-D-glucopyranosylamine (NAG) (K(i) = 32 microM), has been previously characterized by biochemical, biological and crystallographic experiments at 2.3 angstroms resolution. Bioisosteric replacement of the acetyl group by trifluoroacetyl group resulted in an inhibitor, N-trifluoroacetyl-beta-D-glucopyranosylamine (NFAG), with a K(i) = 75 microM. To elucidate the structural basis of its reduced potency, we determined the ligand structure in complex with GPb at 1.8 angstroms resolution. To compare the binding mode of N-trifluoroacetyl derivative with that of the lead molecule, we also determined the structure of GPb-NAG complex at a higher resolution (1.9 angstroms). NFAG can be accommodated in the catalytic site of T-state GPb at approximately the same position as that of NAG and stabilize the T-state conformation of the 280 s loop by making several favourable contacts to Asn284 of this loop. The difference observed in the K(i) values of the two 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 interaction, and desolvation effects.


    Related Citations: 
    • N-acetyl-beta-D-glucopyranosylamine: a potent T-state inhibitor of glycogen phosphorylase. A comparison with alpha-D-glucose
      Oikonomakos, N.G., Kontou, M., Zographos, S.E., Watson, K.A., Johnson, L.N., Bichard, C.J., Fleet, G.W., Acharya, K.R.
      (1995) Protein Sci 4: 2469
    • Glucose analogue inhibitors of glycogen phosphorylase: from crystallographic analysis to drug prediction using GRID force-field and GOLPE variable selection
      Watson, K.A.
      (1995) Acta Crystallogr D Biol Crystallogr 51: 458

    Organizational Affiliation

    Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48, Vas. Constantinou Ave. 116 35 Athens, Greece.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycogen phosphorylase, muscle formA842Oryctolagus cuniculusMutation(s): 0 
Gene Names: PYGM
EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus)
Explore P00489 
Go to UniProtKB:  P00489
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NTF (Subject of Investigation/LOI)
Query on NTF

Download Ideal Coordinates CCD File 
B [auth A]N-(trifluoroacetyl)-beta-D-glucopyranosylamine
C8 H12 F3 N O6
XMUBEPVSEUVEBW-VFUOTHLCSA-N
 Ligand Interaction
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
C [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
NTF Binding MOAD:  1WW3 Ki: 7.50e+4 (nM) from 1 assay(s)
BindingDB:  1WW3 Ki: min: 7.50e+4, max: 8.10e+4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.789α = 90
b = 128.789β = 90
c = 116.234γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    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: Database references, Derived calculations, Structure summary