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: | 5.200 | 5.200 | 5.200 | 0.000 | 5.200 | 1 |
| 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: | 8.173 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.249 | 276.750 |
| % Hydrophobic | % Polar |
|---|---|
| 31.71 | 68.29 |
| According to VolSite | |
| HET Code: | 8UP |
|---|---|
| Formula: | C15H18BrN2O2 |
| Molecular weight: | 338.220 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.62 % |
| Polar Surface area: | 70.07 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -5.8686 | -17.5039 | 6.64235 |
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 |
| BR | CD | LYS- 142 | 4.33 | 0 | Hydrophobic |
| BR | CB | SER- 145 | 3.97 | 0 | Hydrophobic |
| C15 | OD2 | ASP- 192 | 3.44 | 0 | Ionic (Ligand Cationic) |
| C15 | OD1 | ASP- 192 | 3.94 | 0 | Ionic (Ligand Cationic) |
| N2 | OD2 | ASP- 192 | 2.93 | 135.68 | H-Bond (Ligand Donor) |
| N1 | OD2 | ASP- 192 | 3.27 | 126.94 | H-Bond (Ligand Donor) |
| N1 | OD1 | ASP- 192 | 3.04 | 150.66 | H-Bond (Ligand Donor) |
| N1 | OG | SER- 193 | 2.82 | 132.19 | H-Bond (Ligand Donor) |
| C14 | CB | GLN- 195 | 4.02 | 0 | Hydrophobic |
| C1 | CG | GLN- 195 | 3.75 | 0 | Hydrophobic |
| C2 | CB | GLN- 195 | 3.76 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 216 | 3.69 | 0 | Hydrophobic |
| N2 | O | GLY- 221 | 2.87 | 151 | H-Bond (Ligand Donor) |
| C11 | SG | CYS- 222 | 4.44 | 0 | Hydrophobic |
| C9 | SG | CYS- 222 | 3.9 | 0 | Hydrophobic |
| C13 | SG | CYS- 222 | 3.76 | 0 | Hydrophobic |
| N2 | O | HOH- 405 | 3.25 | 123.13 | H-Bond (Ligand Donor) |
