sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2001-09-12
| 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 | 10 % |
| B | 90 % |
| B-Factor: | 9.773 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.700 | 725.625 |
| % Hydrophobic | % Polar |
|---|---|
| 37.21 | 62.79 |
| According to VolSite | |
| HET Code: | SOX |
|---|---|
| Formula: | C16H19N2O5S |
| Molecular weight: | 351.397 g/mol |
| DrugBank ID: | DB08559 |
| Buried Surface Area: | 64.72 % |
| Polar Surface area: | 113.97 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 14.8323 | -1.0865 | 1.61975 |
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 |
| C19 | CB | SER- 1 | 3.81 | 0 | Hydrophobic |
| C19 | CB | PRO- 22 | 3.9 | 0 | Hydrophobic |
| C17 | CE1 | PHE- 24 | 3.84 | 0 | Hydrophobic |
| C21 | CB | SER- 67 | 3.62 | 0 | Hydrophobic |
| O16 | N | ALA- 69 | 2.84 | 156.48 | H-Bond (Protein Donor) |
| C18 | CB | ALA- 69 | 3.91 | 0 | Hydrophobic |
| C23 | CB | ALA- 69 | 3.69 | 0 | Hydrophobic |
| C10 | CZ | PHE- 71 | 3.59 | 0 | Hydrophobic |
| C21 | CE | MET- 142 | 4.12 | 0 | Hydrophobic |
| C22 | SD | MET- 142 | 3.56 | 0 | Hydrophobic |
| C17 | CE1 | PHE- 146 | 3.57 | 0 | Hydrophobic |
| C23 | CB | PHE- 146 | 4.15 | 0 | Hydrophobic |
| C23 | CD2 | PHE- 146 | 3.48 | 0 | Hydrophobic |
| C21 | CG2 | ILE- 177 | 4.45 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 177 | 4.06 | 0 | Hydrophobic |
| O16 | ND2 | ASN- 241 | 3 | 157.02 | H-Bond (Protein Donor) |
| C10 | CE2 | PHE- 256 | 4.13 | 0 | Hydrophobic |
| O12 | CZ | ARG- 263 | 3.82 | 0 | Ionic (Protein Cationic) |
| O13 | ND2 | ASN- 388 | 3.43 | 165.56 | H-Bond (Protein Donor) |
| O12 | ND2 | ASN- 388 | 3.42 | 125.27 | H-Bond (Protein Donor) |
