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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:

4br7

1.800 Å

X-ray

2013-06-04

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Ectonucleoside triphosphate diphosphohydrolase I
ID:Q5ZUA2_LEGPH
AC:Q5ZUA2
Organism:Legionella pneumophila subsp. pneumophila
Reign:Bacteria
TaxID:272624
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:27.916
Number of residues:27
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.224705.375

% Hydrophobic% Polar
23.9276.08
According to VolSite

Ligand :
4br7_1 Structure
HET Code: AU1
Formula: C10H13N6O9P2
Molecular weight: 423.193 g/mol
DrugBank ID: -
Buried Surface Area:43.99 %
Polar Surface area: 263.51 Å2
Number of
H-Bond Acceptors: 13
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
33.922331.26730.2941


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
O1BOG1THR- 533.34164.37H-Bond
(Protein Donor)
O2BNZLYS- 803.750Ionic
(Protein Cationic)
O3BNZLYS- 823.930Ionic
(Protein Cationic)
N3NE2GLN- 2312.81138.95H-Bond
(Protein Donor)
C2'CZTYR- 3463.980Hydrophobic
N6OHTYR- 3502.92159.52H-Bond
(Ligand Donor)