2QNB

Glycogen Phosphorylase b in complex with N-benzoyl-N'-beta-D-glucopyranosyl urea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

N-(4-substituted-benzoyl)-N'-(beta-D-glucopyranosyl)ureas, inhibitors of glycogen phosphorylase: synthesis, kinetic and crystallographic evaluation

Nagy, V.Felf ldi, N.Praly, J.-P.Docsa, T.Gergerly, P.Chrysina, E.D.Tiraidis, C.Kosmopoulou, M.N.Alexacou, K.-M.Konstantakaki, M.

To be published.

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
Find proteins for P00489 (Oryctolagus cuniculus)
Explore P00489 
Go to UniProtKB:  P00489
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BZD
Query on BZD

Download CCD File 
A
N-[(phenylcarbonyl)carbamoyl]-beta-D-glucopyranosylamine
C14 H18 N2 O7
JSBCZGSPFATCOV-BZNQNGANSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
AL-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BZDKi :  4600   nM  PDBBind
BZDKi:  4600   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.653α = 90
b = 128.653β = 90
c = 116.75γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary