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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:

4gpb

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:26.826
Number of residues:33
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 1
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.361607.500

% Hydrophobic% Polar
36.1163.89
According to VolSite

Ligand :
4gpb_1 Structure
HET Code: GFP
Formula: C6H10FO8P
Molecular weight: 260.111 g/mol
DrugBank ID: -
Buried Surface Area:68.26 %
Polar Surface area: 152.15 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 3
Rings: 1
Aromatic rings: 0
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
32.96922.73227.4065


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- 1352.84162.42H-Bond
(Protein Donor)
C6CBLEU- 1364.490Hydrophobic
O3PNLEU- 1362.79167.74H-Bond
(Protein Donor)
C6CD2LEU- 1394.280Hydrophobic
C1CBHIS- 3774.450Hydrophobic
O6ND1HIS- 3772.71179.77H-Bond
(Ligand Donor)
O6ND2ASN- 4842.96143.94H-Bond
(Protein Donor)
F2CZTYR- 5734.180Hydrophobic
O3OE1GLU- 6722.87163.95H-Bond
(Ligand Donor)
C3CBALA- 6734.430Hydrophobic
C4CBSER- 6744.220Hydrophobic
O3NSER- 6743.13159.69H-Bond
(Protein Donor)
O3NGLY- 6753.29133.84H-Bond
(Protein Donor)
O4NGLY- 6752.67142.41H-Bond
(Protein Donor)
O3POHOH- 14202.97179.99H-Bond
(Protein Donor)