sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2005-04-21
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.340 | 8.340 | 8.340 | 0.000 | 8.340 | 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 |
|---|---|
| A | 100 % |
| B-Factor: | 31.247 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.596 | 664.875 |
| % Hydrophobic | % Polar |
|---|---|
| 37.56 | 62.44 |
| According to VolSite | |
| HET Code: | 382 |
|---|---|
| Formula: | C22H23F2N7O |
| Molecular weight: | 439.461 g/mol |
| DrugBank ID: | DB04591 |
| Buried Surface Area: | 59.15 % |
| Polar Surface area: | 93.69 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 16.3654 | -14.1801 | 22.7262 |
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 |
| C26 | CD1 | LEU- 99 | 4.4 | 0 | Hydrophobic |
| C1 | CG | LEU- 99 | 3.7 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 174 | 4.12 | 0 | Hydrophobic |
| C40 | CB | ALA- 190 | 3.68 | 0 | Hydrophobic |
| O33 | OG | SER- 195 | 3.38 | 128.04 | H-Bond (Protein Donor) |
| C34 | CB | SER- 195 | 4.42 | 0 | Hydrophobic |
| C39 | CG1 | VAL- 213 | 3.63 | 0 | Hydrophobic |
| C5 | CE3 | TRP- 215 | 3.78 | 0 | Hydrophobic |
| C6 | CD2 | TRP- 215 | 3.92 | 0 | Hydrophobic |
| F18 | CE3 | TRP- 215 | 3.89 | 0 | Hydrophobic |
| N20 | O | GLY- 216 | 3.33 | 150.13 | H-Bond (Ligand Donor) |
| F18 | CG | GLU- 217 | 3.6 | 0 | Hydrophobic |
| C42 | SG | CYS- 220 | 3.93 | 0 | Hydrophobic |
