sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.020 Å
X-ray
2004-07-30
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.880 | 5.890 | 5.890 | 0.010 | 5.900 | 2 |
| Name: | Urokinase-type plasminogen activator |
|---|---|
| ID: | UROK_HUMAN |
| AC: | P00749 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.21.73 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 5.598 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.231 | 256.500 |
| % Hydrophobic | % Polar |
|---|---|
| 22.37 | 77.63 |
| According to VolSite | |
| HET Code: | 745 |
|---|---|
| Formula: | C20H19N2 |
| Molecular weight: | 287.378 g/mol |
| DrugBank ID: | DB03476 |
| Buried Surface Area: | 49.46 % |
| Polar Surface area: | 51.61 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 22.6573 | 16.3055 | 32.5929 |
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 |
| C17 | OD1 | ASP- 191 | 3.79 | 0 | Ionic (Ligand Cationic) |
| C17 | OD2 | ASP- 191 | 3.35 | 0 | Ionic (Ligand Cationic) |
| N18 | OD1 | ASP- 191 | 2.84 | 144.48 | H-Bond (Ligand Donor) |
| N19 | OD2 | ASP- 191 | 2.93 | 122.01 | H-Bond (Ligand Donor) |
| N18 | OG | SER- 192 | 2.71 | 143.84 | H-Bond (Ligand Donor) |
| C7 | CG | GLN- 194 | 4.15 | 0 | Hydrophobic |
| C23 | CB | GLN- 194 | 3.88 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 215 | 3.89 | 0 | Hydrophobic |
| N19 | O | GLY- 220 | 3.06 | 135.41 | H-Bond (Ligand Donor) |
| C5 | SG | CYS- 221 | 4.4 | 0 | Hydrophobic |
| C13 | SG | CYS- 221 | 4.06 | 0 | Hydrophobic |
