5O50

Glycogen Phosphorylase b in complex with 33a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.130 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Nanomolar Inhibitors of Glycogen Phosphorylase Based on beta-d-Glucosaminyl Heterocycles: A Combined Synthetic, Enzyme Kinetic, and Protein Crystallography Study.

Bokor, E.Kyriakis, E.Solovou, T.G.A.Koppany, C.Kantsadi, A.L.Szabo, K.E.Szakacs, A.Stravodimos, G.A.Docsa, T.Skamnaki, V.T.Zographos, S.E.Gergely, P.Leonidas, D.D.Somsak, L.

(2017) J. Med. Chem. 60: 9251-9262

  • DOI: 10.1021/acs.jmedchem.7b01056
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aryl substituted 1-(β-d-glucosaminyl)-1,2,3-triazoles as well as C-β-d-glucosaminyl 1,2,4-triazoles and imidazoles were synthesized and tested as inhibitors against muscle and liver isoforms of glycogen phosphorylase (GP). While the N-β-d-glucosaminy ...

    Aryl substituted 1-(β-d-glucosaminyl)-1,2,3-triazoles as well as C-β-d-glucosaminyl 1,2,4-triazoles and imidazoles were synthesized and tested as inhibitors against muscle and liver isoforms of glycogen phosphorylase (GP). While the N-β-d-glucosaminyl 1,2,3-triazoles showed weak or no inhibition, the C-β-d-glucosaminyl derivatives had potent activity, and the best inhibitor was the 2-(β-d-glucosaminyl)-4(5)-(2-naphthyl)-imidazole with a K i value of 143 nM against human liver GPa. An X-ray crystallography study of the rabbit muscle GPb inhibitor complexes revealed structural features of the strong binding and offered an explanation for the differences in inhibitory potency between glucosyl and glucosaminyl derivatives and also for the differences between imidazole and 1,2,4-triazole analogues.


    Organizational Affiliation

    Department of Organic Chemistry, University of Debrecen , POB 400, H-4002 Debrecen, Hungary.,Department of Medical Chemistry, Faculty of Medicine, University of Debrecen , Egyetem tér 1, H-4032 Debrecen, Hungary.,Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation , 48 Vassileos Constantinou Avenue, 11635 Athens, Greece.,Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis , 41500 Larissa, 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMP
Query on IMP

Download SDF File 
Download CCD File 
A
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
 Ligand Interaction
9L2
Query on 9L2

Download SDF File 
Download CCD File 
A
(2~{R},3~{S},4~{R},5~{R},6~{R})-5-azanyl-2-(hydroxymethyl)-6-(4-phenyl-1~{H}-imidazol-2-yl)oxane-3,4-diol
C15 H19 N3 O4
XNWVPLWFFIGCKG-DHGKCCLASA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.130 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.480α = 90.00
b = 128.480β = 90.00
c = 116.260γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2017-11-29
    Type: Database references