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
2004-07-01
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.300 | 6.300 | 6.300 | 0.000 | 6.300 | 1 |
| 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: | 28.523 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.571 | 681.750 |
| % Hydrophobic | % Polar |
|---|---|
| 41.09 | 58.91 |
| According to VolSite | |
| HET Code: | PTB |
|---|---|
| Formula: | C11H18N3O2 |
| Molecular weight: | 224.280 g/mol |
| DrugBank ID: | DB03833 |
| Buried Surface Area: | 63.91 % |
| Polar Surface area: | 72.59 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 21.5828 | 1.12775 | -8.14387 |
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 | 2.79 | 169.41 | H-Bond (Ligand Donor) |
| O | N | GLY- 46 | 3.05 | 157.03 | H-Bond (Protein Donor) |
| C9 | CB | SER- 113 | 3.58 | 0 | Hydrophobic |
| O | N | TRP- 114 | 2.87 | 138.36 | H-Bond (Protein Donor) |
| CG | CE1 | PHE- 139 | 3.71 | 0 | Hydrophobic |
| CG | CD2 | TYR- 149 | 4.02 | 0 | Hydrophobic |
| CG | CE2 | TYR- 150 | 4.49 | 0 | Hydrophobic |
| N | OE2 | GLU- 204 | 3.2 | 164.26 | H-Bond (Ligand Donor) |
| N | OE1 | GLU- 204 | 3.13 | 134.42 | H-Bond (Ligand Donor) |
| N | OE2 | GLU- 204 | 3.2 | 0 | Ionic (Ligand Cationic) |
| N | OE1 | GLU- 204 | 3.13 | 0 | Ionic (Ligand Cationic) |
| CG | CZ | PHE- 236 | 4.23 | 0 | Hydrophobic |
| CB | SG | CYS- 271 | 3.86 | 0 | Hydrophobic |
