Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

4pd6

2.080 Å

X-ray

2014-04-17

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:34.380
Number of residues:28
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.700924.750

% Hydrophobic% Polar
63.1436.86
According to VolSite

Ligand :
4pd6_1 Structure
HET Code: URI
Formula: C9H12N2O6
Molecular weight: 244.201 g/mol
DrugBank ID: DB02745
Buried Surface Area:62.07 %
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
51.4091-19.5246-8.43271


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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- 1543.08162.19H-Bond
(Protein Donor)
C5'CBASN- 3314.20Hydrophobic
O3'OE1GLU- 3322.74147.39H-Bond
(Ligand Donor)
O5'OE2GLU- 3322.69170.18H-Bond
(Ligand Donor)
C5'CBPHE- 3333.920Hydrophobic
C2'CGPHE- 3663.890Hydrophobic
C3'CD1PHE- 3663.590Hydrophobic
O3'ND2ASN- 3683.09145.15H-Bond
(Protein Donor)
O2'OGSER- 3712.78160.36H-Bond
(Ligand Donor)
C1'CD1ILE- 3743.640Hydrophobic
N3OHOH- 6282.94175.97H-Bond
(Ligand Donor)