sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2012-06-28
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.200 | 6.200 | 6.200 | 0.000 | 6.200 | 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: | 12.067 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.351 | 303.750 |
| % Hydrophobic | % Polar |
|---|---|
| 28.89 | 71.11 |
| According to VolSite | |
| HET Code: | UI3 |
|---|---|
| Formula: | C16H17N4O3S |
| Molecular weight: | 345.396 g/mol |
| DrugBank ID: | DB03046 |
| Buried Surface Area: | 57.43 % |
| Polar Surface area: | 121.18 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -5.29067 | -18.3044 | 5.99746 |
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 |
| C37 | CD | LYS- 142 | 4.34 | 0 | Hydrophobic |
| C37 | CB | SER- 145 | 3.91 | 0 | Hydrophobic |
| C16 | OD2 | ASP- 192 | 3.62 | 0 | Ionic (Ligand Cationic) |
| C16 | OD1 | ASP- 192 | 3.85 | 0 | Ionic (Ligand Cationic) |
| N17 | OD2 | ASP- 192 | 3.07 | 141.53 | H-Bond (Ligand Donor) |
| N18 | OD2 | ASP- 192 | 3.45 | 130.2 | H-Bond (Ligand Donor) |
| N18 | OD1 | ASP- 192 | 2.95 | 148.36 | H-Bond (Ligand Donor) |
| N18 | OG | SER- 193 | 2.85 | 129.52 | H-Bond (Ligand Donor) |
| C37 | SG | CYS- 194 | 3.91 | 0 | Hydrophobic |
| C20 | CG | GLN- 195 | 3.86 | 0 | Hydrophobic |
| C6 | CB | GLN- 195 | 3.76 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 216 | 3.82 | 0 | Hydrophobic |
| N17 | O | GLY- 221 | 2.78 | 147.45 | H-Bond (Ligand Donor) |
| C12 | SG | CYS- 222 | 3.91 | 0 | Hydrophobic |
| C37 | SG | CYS- 222 | 4.09 | 0 | Hydrophobic |
| N17 | O | HOH- 408 | 3.45 | 123.9 | H-Bond (Ligand Donor) |
| N27 | O | HOH- 439 | 3.33 | 153.85 | H-Bond (Protein Donor) |
