sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2004-07-06
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.800 | 8.800 | 8.800 | 0.000 | 8.800 | 1 |
| Name: | Bacterial leucyl aminopeptidase |
|---|---|
| ID: | AMPX_VIBPR |
| AC: | Q01693 |
| Organism: | Vibrio proteolyticus |
| Reign: | Bacteria |
| TaxID: | 671 |
| EC Number: | 3.4.11.10 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 12.918 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.489 | 310.500 |
| % Hydrophobic | % Polar |
|---|---|
| 47.83 | 52.17 |
| According to VolSite | |
| HET Code: | BES |
|---|---|
| Formula: | C16H24N2O4 |
| Molecular weight: | 308.373 g/mol |
| DrugBank ID: | DB03424 |
| Buried Surface Area: | 67.93 % |
| Polar Surface area: | 117.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 35.3084 | -3.46241 | 43.7268 |
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 | OE1 | GLU- 151 | 2.97 | 158.74 | H-Bond (Ligand Donor) |
| C15 | CD2 | LEU- 155 | 3.31 | 0 | Hydrophobic |
| C1 | SD | MET- 180 | 4.23 | 0 | Hydrophobic |
| C12 | SD | MET- 180 | 4.08 | 0 | Hydrophobic |
| C8 | SG | CYS- 223 | 3.82 | 0 | Hydrophobic |
| C13 | CE2 | TYR- 225 | 4.16 | 0 | Hydrophobic |
| O4 | OH | TYR- 225 | 2.66 | 163.05 | H-Bond (Protein Donor) |
| C8 | SG | CYS- 227 | 4 | 0 | Hydrophobic |
| C6 | CB | CYS- 227 | 4.19 | 0 | Hydrophobic |
| N1 | O | CYS- 227 | 2.76 | 165.08 | H-Bond (Ligand Donor) |
| C8 | CE | MET- 242 | 4.37 | 0 | Hydrophobic |
| C10 | CZ | PHE- 244 | 3.28 | 0 | Hydrophobic |
| C10 | CE1 | PHE- 248 | 3.47 | 0 | Hydrophobic |
| C10 | CB | TYR- 251 | 4.13 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 255 | 4.04 | 0 | Hydrophobic |
| O2 | ZN | ZN- 501 | 2.07 | 0 | Metal Acceptor |
| O3 | ZN | ZN- 501 | 2.29 | 0 | Metal Acceptor |
| O2 | ZN | ZN- 502 | 1.94 | 0 | Metal Acceptor |
