sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2005-04-22
| Name: | Proline iminopeptidase |
|---|---|
| ID: | PIP_SERMA |
| AC: | O32449 |
| Organism: | Serratia marcescens |
| Reign: | Bacteria |
| TaxID: | 615 |
| EC Number: | 3.4.11.5 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 31.533 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.564 | 560.250 |
| % Hydrophobic | % Polar |
|---|---|
| 42.17 | 57.83 |
| According to VolSite | |
| HET Code: | STX |
|---|---|
| Formula: | C9H16N3O2 |
| Molecular weight: | 198.242 g/mol |
| DrugBank ID: | DB08576 |
| Buried Surface Area: | 58.37 % |
| Polar Surface area: | 72.59 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 22.1291 | 1.31636 | -8.32993 |
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 |
| N | O | GLY- 46 | 3.11 | 168.6 | H-Bond (Ligand Donor) |
| O | N | GLY- 46 | 3.05 | 153.88 | H-Bond (Protein Donor) |
| C8 | CB | SER- 113 | 3.88 | 0 | Hydrophobic |
| O | N | TRP- 114 | 2.89 | 139.71 | H-Bond (Protein Donor) |
| N | OE1 | GLU- 204 | 3.09 | 132.43 | H-Bond (Ligand Donor) |
| N | OE1 | GLU- 232 | 3.16 | 0 | Ionic (Ligand Cationic) |
