sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.470 Å
X-ray
2008-01-04
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.340 | 5.340 | 5.340 | 0.000 | 5.340 | 1 |
| Name: | Prothrombin |
|---|---|
| ID: | THRB_HUMAN |
| AC: | P00734 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.21.5 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| H | 100 % |
| B-Factor: | 20.481 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.755 | 411.750 |
| % Hydrophobic | % Polar |
|---|---|
| 45.08 | 54.92 |
| According to VolSite | |
| HET Code: | 53U |
|---|---|
| Formula: | C21H26N3O2 |
| Molecular weight: | 352.450 g/mol |
| DrugBank ID: | DB07143 |
| Buried Surface Area: | 58.57 % |
| Polar Surface area: | 77.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 17.1225 | -12.6012 | 22.4623 |
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 |
| C5 | CZ | TYR- 60 | 3.65 | 0 | Hydrophobic |
| C6 | CH2 | TRP- 60 | 3.78 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 99 | 4.23 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 99 | 4.11 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 99 | 4.02 | 0 | Hydrophobic |
| C21 | CD1 | ILE- 174 | 3.67 | 0 | Hydrophobic |
| C12 | CB | ALA- 190 | 3.86 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 213 | 3.58 | 0 | Hydrophobic |
| N3 | O | SER- 214 | 2.82 | 175.63 | H-Bond (Ligand Donor) |
| C1 | CE3 | TRP- 215 | 4.32 | 0 | Hydrophobic |
| C21 | CB | TRP- 215 | 3.73 | 0 | Hydrophobic |
| N1 | O | GLY- 216 | 2.9 | 168.07 | H-Bond (Ligand Donor) |
| O1 | N | GLY- 216 | 2.96 | 165.73 | H-Bond (Protein Donor) |
| C14 | SG | CYS- 220 | 4.17 | 0 | Hydrophobic |
