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: | 7.200 | 7.200 | 7.200 | 0.000 | 7.200 | 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: | 9.993 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.553 | 516.375 |
| % Hydrophobic | % Polar |
|---|---|
| 27.45 | 72.55 |
| According to VolSite | |
| HET Code: | 7UP |
|---|---|
| Formula: | C22H21N3 |
| Molecular weight: | 327.422 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 49.62 % |
| Polar Surface area: | 68.22 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -3.85848 | -15.0992 | 8.48488 |
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 |
| C20 | CB | HIS- 46 | 4.1 | 0 | Hydrophobic |
| N3 | OD2 | ASP- 50 | 2.76 | 169.32 | H-Bond (Ligand Donor) |
| N3 | OD2 | ASP- 50 | 2.76 | 0 | Ionic (Ligand Cationic) |
| N2 | OD2 | ASP- 192 | 2.92 | 140.99 | H-Bond (Ligand Donor) |
| N1 | OD1 | ASP- 192 | 3.09 | 151.05 | H-Bond (Ligand Donor) |
| C1 | OD2 | ASP- 192 | 3.6 | 0 | Ionic (Ligand Cationic) |
| C1 | OD1 | ASP- 192 | 3.86 | 0 | Ionic (Ligand Cationic) |
| N1 | OG | SER- 193 | 2.85 | 127.1 | H-Bond (Ligand Donor) |
| C8 | CB | GLN- 195 | 3.62 | 0 | Hydrophobic |
| C12 | CG | GLN- 195 | 3.92 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 216 | 3.91 | 0 | Hydrophobic |
| N2 | O | GLY- 221 | 2.92 | 157.13 | H-Bond (Ligand Donor) |
| C11 | SG | CYS- 222 | 3.73 | 0 | Hydrophobic |
