sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2000-07-06
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.190 | 6.190 | 6.190 | 0.000 | 6.190 | 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: | 22.976 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.085 | 249.750 |
| % Hydrophobic | % Polar |
|---|---|
| 27.03 | 72.97 |
| According to VolSite | |
| HET Code: | UKP |
|---|---|
| Formula: | C32H50N6O4S |
| Molecular weight: | 614.842 g/mol |
| DrugBank ID: | DB04172 |
| Buried Surface Area: | 50.26 % |
| Polar Surface area: | 174.42 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| 29.935 | 10.9492 | 29.2949 |
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 |
| C22 | CB | HIS- 57 | 3.9 | 0 | Hydrophobic |
| N24 | OH | TYR- 94 | 3.16 | 156.06 | H-Bond (Ligand Donor) |
| C12 | CD2 | LEU- 97 | 4.49 | 0 | Hydrophobic |
| C14 | CG | LEU- 97 | 4.46 | 0 | Hydrophobic |
| CX | OD1 | ASP- 189 | 3.86 | 0 | Ionic (Ligand Cationic) |
| CX | OD2 | ASP- 189 | 3.31 | 0 | Ionic (Ligand Cationic) |
| NX1 | OD1 | ASP- 189 | 2.79 | 130.15 | H-Bond (Ligand Donor) |
| NX1 | OD2 | ASP- 189 | 2.89 | 132.58 | H-Bond (Ligand Donor) |
| NX2 | OD2 | ASP- 189 | 2.83 | 132.6 | H-Bond (Ligand Donor) |
| NX1 | OG | SER- 190 | 2.83 | 148.25 | H-Bond (Ligand Donor) |
| CB | CB | GLN- 192 | 3.7 | 0 | Hydrophobic |
| CE2 | CG1 | VAL- 213 | 3.65 | 0 | Hydrophobic |
| C13 | CB | TRP- 215 | 4.26 | 0 | Hydrophobic |
| O | N | GLY- 216 | 3.48 | 132.85 | H-Bond (Protein Donor) |
| NX2 | O | GLY- 219 | 3.08 | 143.16 | H-Bond (Ligand Donor) |
| OS1 | N | GLY- 219 | 2.82 | 158.21 | H-Bond (Protein Donor) |
| CD1 | SG | CYS- 220 | 4.03 | 0 | Hydrophobic |
