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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:

3tij

2.440 Å

X-ray

2011-08-20

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Nucleoside permease
ID:Q9KPL5_VIBCH
AC:Q9KPL5
Organism:Vibrio cholerae serotype O1
Reign:Bacteria
TaxID:243277
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:46.536
Number of residues:28
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.859347.625

% Hydrophobic% Polar
59.2240.78
According to VolSite

Ligand :
3tij_1 Structure
HET Code: URI
Formula: C9H12N2O6
Molecular weight: 244.201 g/mol
DrugBank ID: DB02745
Buried Surface Area:62.29 %
Polar Surface area: 119.33 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 4
Rings: 2
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
51.3141-19.4992-8.47059


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
O2NE2GLN- 1542.87160.72H-Bond
(Protein Donor)
C5'CBASN- 3314.240Hydrophobic
O3'OE1GLU- 3322.68168.23H-Bond
(Ligand Donor)
O5'OE2GLU- 3322.67168.54H-Bond
(Ligand Donor)
C5'CBPHE- 3333.960Hydrophobic
C2'CGPHE- 3663.860Hydrophobic
C3'CD1PHE- 3663.60Hydrophobic
O3'ND2ASN- 3683.11144.09H-Bond
(Protein Donor)
O2'OGSER- 3712.69160.33H-Bond
(Ligand Donor)
C1'CD1ILE- 3743.880Hydrophobic
N3OHOH- 4262.84177.31H-Bond
(Ligand Donor)