1H5U

THE 1.76 A RESOLUTION CRYSTAL STRUCTURE OF GLYCOGEN PHOSPHORYLASE B COMPLEXED WITH GLUCOSE AND CP320626, A POTENTIAL ANTIDIABETIC DRUG

Structural Biology Knowledgebase: 1H5U SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.211

Literature

Macromolecules
Sequence Display for 1H5U

Classification: GLYCOGEN METABOLISM

Total Structure Weight: 98163.18

Macromolecule Entities
Molecule Chains Length Organism Details
GLYCOGEN PHOSPHORYLASE A 842 Oryctolagus cuniculus EC#: 2.4.1.1 IUBMB
Mutation: L380I
Gene Name(s): PYGM Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CHI
Query on CHI

A 5-CHLORO-1H-INDOLE-2-CARBOXYLIC ACID [1-(4- FLUOROBENZYL)-2-(4-HYDROXYPIPERIDIN-1YL)- 2-OXOETHYL]AMIDE
C23 H23 Cl F N3 O3
YDCGVASFVACWKF-NRFANRHFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PLP
Query on PLP

A PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate (Synonym)
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GLC
Query on GLC

A ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
CHI IC50: 500 nM (97) BindingDB

IC50: 178 nM  BindingMOAD
IC50: 178 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.211
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 128.97 α = 90.00
b = 128.97 β = 90.00
c = 116.19 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-05-25
  • Released Date: 2001-06-28
  • Deposition author(s): Oikonomakos, N.G., Zographos, S.E., Skamnaki, V.T., Archontis, G.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4