5MEM

A potent fluorescent inhibitor of glycogen phosphorylase as a catalytic site probe.

  • Classification: FLUORESCENT PROTEIN
  • Organism(s): Oryctolagus cuniculus
  • Mutation(s): No 

  • Deposited: 2016-11-15 Released: 2017-11-29 
  • Deposition Author(s): Mamais, M., Chrysina, E.D.
  • Funding Organization(s): European Social Fund, Greek National Strategic Reference Framework (NSRF) - Research Funding Program: Heracleitus II, European Union

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A New Potent Inhibitor of Glycogen Phosphorylase Reveals the Basicity of the Catalytic Site.

Mamais, M.Degli Esposti, A.Kouloumoundra, V.Gustavsson, T.Monti, F.Venturini, A.Chrysina, E.D.Markovitsi, D.Gimisis, T.

(2017) Chemistry 23: 8800-8805

  • DOI: 10.1002/chem.201701591
  • Primary Citation of Related Structures:  
    5MEM

  • PubMed Abstract: 
  • The design and synthesis of a glucose-based acridone derivative (GLAC), a potent inhibitor of glycogen phosphorylase (GP) are described. GLAC is the first inhibitor of glycogen phosphorylase, the electronic absorption properties of which are clearly distinguishable from those of the enzyme ...

    The design and synthesis of a glucose-based acridone derivative (GLAC), a potent inhibitor of glycogen phosphorylase (GP) are described. GLAC is the first inhibitor of glycogen phosphorylase, the electronic absorption properties of which are clearly distinguishable from those of the enzyme. This allows probing subtle interactions in the catalytic site. The GLAC absorption spectra, associated with X-ray crystallography and quantum chemistry calculations, reveal that part of the catalytic site of GP behaves as a highly basic environment in which GLAC exists as a bis-anion. This is explained by water-bridged hydrogen-bonding interactions with specific catalytic site residues.


    Organizational Affiliation

    Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycogen phosphorylase, muscle formA843Oryctolagus 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
7LS
Query on 7LS

Download Ideal Coordinates CCD File 
C [auth A]2-[[1-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-2-oxidanylidene-pyrimidin-4-yl]amino]-10~{H}-acridin-9-one
C23 H22 N4 O7
GFASNZAXNSUSSV-RECXWPGBSA-N
 Ligand Interaction
PLP
Query on PLP

Download Ideal Coordinates CCD File 
B [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
7LSKi:  71   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.363α = 90
b = 128.363β = 90
c = 116.512γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Social Fund, Greek National Strategic Reference Framework (NSRF) - Research Funding Program: Heracleitus IIGreeceHeracleitus II -MIS:346942
European UnionGreece245866
European UnionGermany283570

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-29
    Type: Initial release