sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2004-03-19
| 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: | 8.059 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.458 | 519.750 |
| % Hydrophobic | % Polar |
|---|---|
| 21.43 | 78.57 |
| According to VolSite | |
| HET Code: | UI3 |
|---|---|
| Formula: | C16H17N4O3S |
| Molecular weight: | 345.396 g/mol |
| DrugBank ID: | DB03046 |
| Buried Surface Area: | 59.14 % |
| 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 |
|---|---|---|
| 22.2346 | 18.0651 | 34.984 |
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- 141 | 3.73 | 0 | Hydrophobic |
| O35 | OG | SER- 144 | 3.46 | 134.29 | H-Bond (Protein Donor) |
| C37 | CB | SER- 144 | 4 | 0 | Hydrophobic |
| C16 | OD1 | ASP- 191 | 3.89 | 0 | Ionic (Ligand Cationic) |
| C16 | OD2 | ASP- 191 | 3.62 | 0 | Ionic (Ligand Cationic) |
| N17 | OD1 | ASP- 191 | 2.89 | 143.31 | H-Bond (Ligand Donor) |
| N17 | OD2 | ASP- 191 | 3.35 | 131.81 | H-Bond (Ligand Donor) |
| N18 | OD2 | ASP- 191 | 3.03 | 143.3 | H-Bond (Ligand Donor) |
| N17 | OG | SER- 192 | 2.92 | 125.18 | H-Bond (Ligand Donor) |
| C37 | SG | CYS- 193 | 3.77 | 0 | Hydrophobic |
| C20 | CG | GLN- 194 | 3.81 | 0 | Hydrophobic |
| C37 | CB | GLN- 194 | 4.43 | 0 | Hydrophobic |
| C6 | CB | GLN- 194 | 3.95 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 215 | 3.86 | 0 | Hydrophobic |
| N18 | O | GLY- 220 | 2.77 | 149.99 | H-Bond (Ligand Donor) |
| C12 | SG | CYS- 221 | 4.06 | 0 | Hydrophobic |
| C37 | SG | CYS- 221 | 4.18 | 0 | Hydrophobic |
