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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

5gpb

2.300 Å

X-ray

1990-06-04

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Glycogen phosphorylase, muscle form
ID:PYGM_RABIT
AC:P00489
Organism:Oryctolagus cuniculus
Reign:Eukaryota
TaxID:9986
EC Number:2.4.1.1


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:21.623
Number of residues:33
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 1
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.422688.500

% Hydrophobic% Polar
37.2562.75
According to VolSite

Ligand :
5gpb_1 Structure
HET Code: GPM
Formula: C7H13O8P
Molecular weight: 256.147 g/mol
DrugBank ID: -
Buried Surface Area:69.72 %
Polar Surface area: 163.15 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 4
Rings: 1
Aromatic rings: 0
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
32.519822.692926.972


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
O2PNGLY- 1352.7157.61H-Bond
(Protein Donor)
C6CD2LEU- 1394.10Hydrophobic
O6ND1HIS- 3772.58155.37H-Bond
(Ligand Donor)
O4ND2ASN- 4843.12127.83H-Bond
(Protein Donor)
O6ND2ASN- 4843.08156.76H-Bond
(Protein Donor)
O3OE1GLU- 6723156.48H-Bond
(Ligand Donor)
C2CBALA- 6734.360Hydrophobic
C4CBSER- 6743.950Hydrophobic
O3NSER- 6742.97156.06H-Bond
(Protein Donor)
O3NGLY- 6752.81130.89H-Bond
(Protein Donor)
O4NGLY- 6752.75132.53H-Bond
(Protein Donor)
O2OHOH- 14522.85156.36H-Bond
(Ligand Donor)