2.080 Å
X-ray
2014-04-17
| Name: | Nucleoside permease |
|---|---|
| ID: | Q9KPL5_VIBCH |
| AC: | Q9KPL5 |
| Organism: | Vibrio cholerae serotype O1 |
| Reign: | Bacteria |
| TaxID: | 243277 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 34.380 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.700 | 924.750 |
| % Hydrophobic | % Polar |
|---|---|
| 63.14 | 36.86 |
| According to VolSite | |

| 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 |
| X | Y | Z |
|---|---|---|
| 51.4091 | -19.5246 | -8.43271 |
Image generated by PoseView
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
| Ligand | Protein | Interaction | |||
|---|---|---|---|---|---|
| Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
| O2 | NE2 | GLN- 154 | 3.08 | 162.19 | H-Bond (Protein Donor) |
| C5' | CB | ASN- 331 | 4.2 | 0 | Hydrophobic |
| O3' | OE1 | GLU- 332 | 2.74 | 147.39 | H-Bond (Ligand Donor) |
| O5' | OE2 | GLU- 332 | 2.69 | 170.18 | H-Bond (Ligand Donor) |
| C5' | CB | PHE- 333 | 3.92 | 0 | Hydrophobic |
| C2' | CG | PHE- 366 | 3.89 | 0 | Hydrophobic |
| C3' | CD1 | PHE- 366 | 3.59 | 0 | Hydrophobic |
| O3' | ND2 | ASN- 368 | 3.09 | 145.15 | H-Bond (Protein Donor) |
| O2' | OG | SER- 371 | 2.78 | 160.36 | H-Bond (Ligand Donor) |
| C1' | CD1 | ILE- 374 | 3.64 | 0 | Hydrophobic |
| N3 | O | HOH- 628 | 2.94 | 175.97 | H-Bond (Ligand Donor) |