sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.650 Å
X-ray
2010-12-16
| Name: | Vanillate porin OpdK |
|---|---|
| ID: | Q9HUR5_PSEAE |
| AC: | Q9HUR5 |
| Organism: | Pseudomonas aeruginosa |
| Reign: | Bacteria |
| TaxID: | 208964 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 26.444 |
|---|---|
| Number of residues: | 19 |
| Including | |
| Standard Amino Acids: | 19 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.330 | 253.125 |
| % Hydrophobic | % Polar |
|---|---|
| 57.33 | 42.67 |
| According to VolSite | |
| HET Code: | VNL |
|---|---|
| Formula: | C8H7O4 |
| Molecular weight: | 167.139 g/mol |
| DrugBank ID: | DB02130 |
| Buried Surface Area: | 59.59 % |
| Polar Surface area: | 69.59 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -25.1855 | 23.3346 | -24.2705 |
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 |
| CZ | CG | LYS- 44 | 4.05 | 0 | Hydrophobic |
| CM1 | CD | LYS- 44 | 3.88 | 0 | Hydrophobic |
| CV | CB | ASP- 59 | 3.81 | 0 | Hydrophobic |
| CM2 | CB | ASP- 59 | 3.7 | 0 | Hydrophobic |
| O3 | O | ALA- 60 | 2.66 | 144.53 | H-Bond (Ligand Donor) |
| CM2 | CB | ILE- 61 | 4.24 | 0 | Hydrophobic |
| CV | CG2 | ILE- 61 | 3.89 | 0 | Hydrophobic |
| CV | CB | ALA- 98 | 4.44 | 0 | Hydrophobic |
| O1 | N | LEU- 114 | 2.94 | 152.86 | H-Bond (Protein Donor) |
| C1 | CD1 | LEU- 114 | 4.03 | 0 | Hydrophobic |
