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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:

5bu2

2.110 Å

X-ray

2015-06-03

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Uncharacterized protein
ID:G8UY02_LEGPN
AC:G8UY02
Organism:Legionella pneumophila subsp. pneumophila ATCC 43290
Reign:Bacteria
TaxID:933093
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C100 %


Ligand binding site composition:

B-Factor:33.257
Number of residues:36
Including
Standard Amino Acids: 35
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.326698.625

% Hydrophobic% Polar
50.7249.28
According to VolSite

Ligand :
5bu2_4 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:61.65 %
Polar Surface area: 260.7 Å2
Number of
H-Bond Acceptors: 14
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
27.435717.0625-20.8991


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
O3'NE2HIS- 3703.04145.77H-Bond
(Ligand Donor)
C3'CG2VAL- 4134.470Hydrophobic
O2BNGLY- 4152.79170.48H-Bond
(Protein Donor)
O2ACZARG- 4163.70Ionic
(Protein Cationic)
C4'CDARG- 4164.380Hydrophobic
O2'NH2ARG- 5103.3169.72H-Bond
(Protein Donor)
O2'OHOH- 8052.97153.01H-Bond
(Protein Donor)