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: | 6.300 | 6.320 | 6.320 | 0.020 | 6.350 | 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: | 7.401 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.143 | 263.250 |
| % Hydrophobic | % Polar |
|---|---|
| 32.05 | 67.95 |
| According to VolSite | |
| HET Code: | 6UP |
|---|---|
| Formula: | C11H12N3 |
| Molecular weight: | 186.233 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.84 % |
| Polar Surface area: | 77.63 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| -20.5181 | -17.9373 | -7.1315 |
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 |
| CAJ | OD2 | ASP- 192 | 3.54 | 0 | Ionic (Ligand Cationic) |
| CAJ | OD1 | ASP- 192 | 3.94 | 0 | Ionic (Ligand Cationic) |
| N2 | OD2 | ASP- 192 | 2.95 | 139.01 | H-Bond (Ligand Donor) |
| N3 | OD2 | ASP- 192 | 3.32 | 127.29 | H-Bond (Ligand Donor) |
| N3 | OD1 | ASP- 192 | 2.97 | 151.13 | H-Bond (Ligand Donor) |
| N3 | OG | SER- 193 | 2.66 | 140.36 | H-Bond (Ligand Donor) |
| CAE | CB | GLN- 195 | 3.7 | 0 | Hydrophobic |
| CAH | CG1 | VAL- 216 | 3.83 | 0 | Hydrophobic |
| N1 | O | GLY- 221 | 3.29 | 168.54 | H-Bond (Ligand Donor) |
| N2 | O | GLY- 221 | 2.88 | 155.37 | H-Bond (Ligand Donor) |
| CAI | SG | CYS- 222 | 3.81 | 0 | Hydrophobic |
