sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2004-10-17
| 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: | 17.047 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.405 | 303.750 |
| % Hydrophobic | % Polar |
|---|---|
| 41.11 | 58.89 |
| According to VolSite | |
| HET Code: | BES |
|---|---|
| Formula: | C16H24N2O4 |
| Molecular weight: | 308.373 g/mol |
| DrugBank ID: | DB03424 |
| Buried Surface Area: | 64.59 % |
| 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 |
|---|---|---|
| 35.2454 | -3.57523 | 43.757 |
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 | 2.77 | 163.61 | H-Bond (Ligand Donor) |
| O2 | OE2 | GLU- 151 | 3.4 | 130.93 | H-Bond (Ligand Donor) |
| C15 | CD2 | LEU- 155 | 3.83 | 0 | Hydrophobic |
| C1 | SD | MET- 180 | 4.31 | 0 | Hydrophobic |
| C12 | SD | MET- 180 | 3.99 | 0 | Hydrophobic |
| C8 | SG | CYS- 223 | 3.81 | 0 | Hydrophobic |
| C13 | CE2 | TYR- 225 | 4.18 | 0 | Hydrophobic |
| O4 | OH | TYR- 225 | 2.55 | 160.53 | H-Bond (Protein Donor) |
| N1 | O | CYS- 227 | 2.87 | 158.52 | H-Bond (Ligand Donor) |
| C8 | CB | CYS- 227 | 4.06 | 0 | Hydrophobic |
| C10 | CZ | PHE- 244 | 3.33 | 0 | Hydrophobic |
| C10 | CB | TYR- 251 | 3.93 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 255 | 3.88 | 0 | Hydrophobic |
| O2 | ZN | ZN- 1001 | 2.16 | 0 | Metal Acceptor |
| O3 | ZN | ZN- 1001 | 2.33 | 0 | Metal Acceptor |
| O2 | ZN | ZN- 1002 | 1.96 | 0 | Metal Acceptor |
