6R0H

Glycogen Phosphorylase b in complex with 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

High Consistency of Structure-Based Design and X-Ray Crystallography: Design, Synthesis, Kinetic Evaluation and Crystallographic Binding Mode Determination of Biphenyl-N-acyl-beta-d-Glucopyranosylamines as Glycogen Phosphorylase Inhibitors.

Fischer, T.Koulas, S.M.Tsagkarakou, A.S.Kyriakis, E.Stravodimos, G.A.Skamnaki, V.T.Liggri, P.G.V.Zographos, S.E.Riedl, R.Leonidas, D.D.

(2019) Molecules 24: --

  • DOI: 10.3390/molecules24071322
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Structure-based design and synthesis of two biphenyl- <i>N </i>-acyl-β-d-glucopyranosylamine derivatives as well as their assessment as inhibitors of human liver glycogen phosphorylase (hlGPa, a pharmaceutical target for type 2 diabetes) is presented ...

    Structure-based design and synthesis of two biphenyl- N -acyl-β-d-glucopyranosylamine derivatives as well as their assessment as inhibitors of human liver glycogen phosphorylase (hlGPa, a pharmaceutical target for type 2 diabetes) is presented. X-ray crystallography revealed the importance of structural water molecules and that the inhibitory efficacy correlates with the degree of disturbance caused by the inhibitor binding to a loop crucial for the catalytic mechanism. The in silico-derived models of the binding mode generated during the design process corresponded very well with the crystallographic data.


    Organizational Affiliation

    Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece. sym.koulas@gmail.com.,Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece. vskamnaki@bio.uth.gr.,Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece. stravodimos@windowslive.com.,Institute of Chemistry and Biotechnology, Center of Organic and Medicinal Chemistry, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland. thomas.fischer@zhaw.ch.,Institute of Chemistry and Biotechnology, Center of Organic and Medicinal Chemistry, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland. rainer.riedl@zhaw.ch.,Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece. b_liggri@windowslive.com.,Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece. kyriakis.ef@gmail.com.,Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece. anastasiatsagk@hotmail.com.,Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece. b_liggri@windowslive.com.,Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece. sez@eie.gr.,Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece. ddleonidas@bio.uth.gr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycogen phosphorylase, muscle form
A
843Oryctolagus 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
JN2
Query on JN2

Download SDF File 
Download CCD File 
A
3-(4-fluorophenyl)-~{N}-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]benzamide
C19 H20 F N O6
ZNFXGMNTWYBCJQ-OGJJZOIMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.159 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.287α = 90.00
b = 128.287β = 90.00
c = 116.120γ = 90.00
Software Package:
Software NamePurpose
CrysalisProdata reduction
Aimlessdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-04-24
    Type: Data collection, Database references