› 2zb2

X-ray diffraction
2.45Å resolution

Human liver glycogen phosphorylase a complexed with glcose and 5-chloro-N-[4-(1,2-dihydroxyethyl)phenyl]-1H-indole-2-carboxamide

Released:
DOI: 10.2210/pdb2zb2/pdb
PDB entry 2zb2 coloured by chain, front view.
PDB entry 2zb2 coloured by chain, side view.
PDB entry 2zb2 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Synthesis of 5-chloro-N-aryl-1H-indole-2-carboxamide derivatives as inhibitors of human liver glycogen phosphorylase a.
Onda K, Suzuki T, Shiraki R, Yonetoku Y, Negoro K, Momose K, Katayama N, Orita M, Yamaguchi T, Ohta M, Tsukamoto S
Bioorg Med Chem 16 5452-64 (2008)
PMID: 18434170

Function and Biology Details

Reaction catalysed: 
((1->4)-alpha-D-glucosyl)(n) + phosphate = ((1->4)-alpha-D-glucosyl)(n-1) + alpha-D-glucose 1-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139193 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glycogen phosphorylase, liver form Chains: A, B
Molecule details ›
Chains: A, B
Length: 849 amino acids
Theoretical weight: 97.42 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P06737 (Residues: 1-847; Coverage: 100%)
Gene name: PYGL
Sequence domains: Carbohydrate phosphorylase
Structure domains: Glycogen Phosphorylase B;

Ligands and Environments


Cofactor: Ligand PLP 2 x PLP
4 bound ligands:
Ligand GLC 2 x GLC
Ligand MES 2 x MES
Ligand A46 2 x A46
Ligand MPD 2 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-6B
Spacegroup: P31
Unit cell:
a: 123.819Å b: 123.819Å c: 123.538Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.3 0.261 0.307
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Glycogen phosphorylase inhibitors: a patent review (2008 - 2012).
Gaboriaud-Kolar et al. (2013)
3 more

2 mentions without citation

Ellagic Acid, Kaempferol, and Quercetin from Acacia nilotica: Promising Combined Drug With Multiple Mechanisms of Action.
Al-Nour et al. (2019)
1 more