3G2N

Crystal structure of N-acylglucosylamine with glycogen phosphorylase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


Literature

Amide-1,2,3-triazole bioisosterism: the glycogen phosphorylase case

Chrysina, E.D., Bokor, E., Alexacou, K.-M., Charavgi, M.-D., Oikonomakos, G.N., Zographos, S.E., Leonidas, D.D., Oikonomakos, N.G., Somsak, L.

(2009) Tetrahedron Asymmetry 20: 733-740


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycogen phosphorylase, muscle form842Oryctolagus cuniculusMutation(s): 0 
EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus)
Explore P00489 
Go to UniProtKB:  P00489
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00489
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OAK
Query on OAK
Download Ideal Coordinates CCD File 
B [auth A]N-(phenylcarbonyl)-beta-D-glucopyranosylamine
C13 H17 N O6
SPYSOSUFGSNSMY-BZNQNGANSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Binding Affinity Annotations 
IDSourceBinding Affinity
OAK BindingDB:  3G2N Ki: min: 8.10e+4, max: 1.44e+5 (nM) from 3 assay(s)
PDBBind:  3G2N Ki: 8.10e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.639α = 90
b = 128.639β = 90
c = 116.353γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-16
    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
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.4: 2023-11-22
    Changes: Data collection