sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.600 Å
X-ray
2003-03-28
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.720 | 6.120 | 6.200 | 0.180 | 6.200 | 6 |
| 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: | 8.018 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.405 | 324.000 |
| % Hydrophobic | % Polar |
|---|---|
| 22.92 | 77.08 |
| According to VolSite | |
| HET Code: | 675 |
|---|---|
| Formula: | C18H16N3O |
| Molecular weight: | 290.339 g/mol |
| DrugBank ID: | DB01977 |
| Buried Surface Area: | 52.54 % |
| Polar Surface area: | 80.71 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 22.6405 | 15.9048 | 32.5329 |
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 |
| C29 | CB | HIS- 54 | 4.27 | 0 | Hydrophobic |
| N18 | OD1 | ASP- 205 | 2.84 | 151.54 | H-Bond (Ligand Donor) |
| N18 | OD2 | ASP- 205 | 3.48 | 122.01 | H-Bond (Ligand Donor) |
| N19 | OD2 | ASP- 205 | 2.86 | 141.08 | H-Bond (Ligand Donor) |
| C17 | OD1 | ASP- 205 | 3.68 | 0 | Ionic (Ligand Cationic) |
| C17 | OD2 | ASP- 205 | 3.52 | 0 | Ionic (Ligand Cationic) |
| N18 | OG | SER- 206 | 2.77 | 127.33 | H-Bond (Ligand Donor) |
| O36 | NE2 | GLN- 208 | 2.89 | 121.2 | H-Bond (Protein Donor) |
| C5 | CB | GLN- 208 | 3.92 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 229 | 3.83 | 0 | Hydrophobic |
| N19 | O | GLY- 234 | 2.93 | 158.61 | H-Bond (Ligand Donor) |
| C13 | SG | CYS- 235 | 3.93 | 0 | Hydrophobic |
