sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2003-03-28
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.600 | 7.620 | 7.620 | 0.020 | 7.630 | 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: | 5.709 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.203 | 293.625 |
| % Hydrophobic | % Polar |
|---|---|
| 24.14 | 75.86 |
| According to VolSite | |
| HET Code: | 303 |
|---|---|
| Formula: | C24H28N4O |
| Molecular weight: | 388.505 g/mol |
| DrugBank ID: | DB02705 |
| Buried Surface Area: | 44.21 % |
| Polar Surface area: | 97.32 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 24.1859 | 14.6341 | 32.18 |
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 |
| C25 | CB | HIS- 45 | 3.82 | 0 | Hydrophobic |
| N34 | OD2 | ASP- 49 | 3.83 | 0 | Ionic (Ligand Cationic) |
| N18 | OD1 | ASP- 191 | 3.01 | 160.17 | H-Bond (Ligand Donor) |
| N18 | OD2 | ASP- 191 | 3.31 | 127.14 | H-Bond (Ligand Donor) |
| N19 | OD2 | ASP- 191 | 2.85 | 141.06 | H-Bond (Ligand Donor) |
| C17 | OD1 | ASP- 191 | 3.95 | 0 | Ionic (Ligand Cationic) |
| C17 | OD2 | ASP- 191 | 3.49 | 0 | Ionic (Ligand Cationic) |
| N18 | OG | SER- 192 | 2.7 | 123.51 | H-Bond (Ligand Donor) |
| C12 | CG | GLN- 194 | 4.37 | 0 | Hydrophobic |
| C11 | CB | GLN- 194 | 3.83 | 0 | Hydrophobic |
| O21 | NE2 | GLN- 194 | 2.76 | 161.91 | H-Bond (Protein Donor) |
| C2 | CG1 | VAL- 215 | 3.84 | 0 | Hydrophobic |
| N19 | O | GLY- 220 | 2.85 | 156.69 | H-Bond (Ligand Donor) |
| C5 | SG | CYS- 221 | 4.1 | 0 | Hydrophobic |
