3G2H

Crystal structure of 1-(beta-D-glucopyranosyl)-4-substituted-1,2,3-triazoles in complex with glycogen phosphorylase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

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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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IMP
Query on IMP
Download Ideal Coordinates CCD File 
D [auth A]INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
KOT
Query on KOT
Download Ideal Coordinates CCD File 
B [auth A]1-beta-D-glucopyranosyl-4-phenyl-1H-1,2,3-triazole
C14 H17 N3 O5
SLCZDPXCZLKLKY-RKQHYHRCSA-N
DMS
Query on DMS
Download Ideal Coordinates CCD File 
C [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-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
KOT BindingDB:  3G2H Ki: min: 1.51e+5, max: 1.62e+5 (nM) from 2 assay(s)
PDBBind:  3G2H Ki: 1.51e+5 (nM) from 1 assay(s)
Binding MOAD:  3G2H Ki: 1.51e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.287α = 90
b = 127.287β = 90
c = 115.615γ = 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