sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.450 Å
X-ray
2001-09-11
| Name: | Penicillin G acylase |
|---|---|
| ID: | PAC_ECOLX |
| AC: | P06875 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 562 |
| EC Number: | 3.5.1.11 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 19 % |
| B | 81 % |
| B-Factor: | 10.105 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.817 | 280.125 |
| % Hydrophobic | % Polar |
|---|---|
| 60.24 | 39.76 |
| According to VolSite | |
| HET Code: | PNN |
|---|---|
| Formula: | C16H17N2O4S |
| Molecular weight: | 333.382 g/mol |
| DrugBank ID: | DB01053 |
| Buried Surface Area: | 48.03 % |
| Polar Surface area: | 114.84 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 14.8055 | -1.72665 | 3.95691 |
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 |
| O16 | OG | SER- 1 | 2.62 | 153.21 | H-Bond (Protein Donor) |
| C19 | CB | SER- 1 | 4.3 | 0 | Hydrophobic |
| C19 | CB | PRO- 22 | 4.12 | 0 | Hydrophobic |
| C18 | CE1 | PHE- 24 | 3.35 | 0 | Hydrophobic |
| C20 | CB | SER- 67 | 3.85 | 0 | Hydrophobic |
| C23 | CB | ALA- 69 | 3.77 | 0 | Hydrophobic |
| C10 | CZ | PHE- 71 | 3.79 | 0 | Hydrophobic |
| C21 | CE | MET- 142 | 3.82 | 0 | Hydrophobic |
| C22 | SD | MET- 142 | 3.66 | 0 | Hydrophobic |
| C9 | CD1 | PHE- 146 | 3.97 | 0 | Hydrophobic |
| S1 | CD1 | PHE- 146 | 3.57 | 0 | Hydrophobic |
| C23 | CB | PHE- 146 | 4.35 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 177 | 3.87 | 0 | Hydrophobic |
| O16 | O | HOH- 2671 | 3.23 | 125.1 | H-Bond (Protein Donor) |
