sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2002-01-17
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 30.098 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.303 | 432.000 |
| % Hydrophobic | % Polar |
|---|---|
| 44.53 | 55.47 |
| According to VolSite | |
| HET Code: | C24 |
|---|---|
| Formula: | C27H30N7O3 |
| Molecular weight: | 500.572 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.59 % |
| Polar Surface area: | 140.95 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 17.4612 | -14.5846 | 24.2484 |
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 |
| C17 | CB | HIS- 57 | 3.89 | 0 | Hydrophobic |
| C17 | CE2 | TYR- 60 | 3.93 | 0 | Hydrophobic |
| C11 | CH2 | TRP- 60 | 4.02 | 0 | Hydrophobic |
| C17 | CH2 | TRP- 60 | 3.66 | 0 | Hydrophobic |
| C25 | CD1 | LEU- 99 | 4.43 | 0 | Hydrophobic |
| C26 | CG | LEU- 99 | 4.05 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 99 | 3.81 | 0 | Hydrophobic |
| C21 | CD1 | LEU- 99 | 3.75 | 0 | Hydrophobic |
| C35 | CD | ARG- 173 | 4.17 | 0 | Hydrophobic |
| C26 | CD1 | ILE- 174 | 4.34 | 0 | Hydrophobic |
| C30 | CG1 | ILE- 174 | 3.85 | 0 | Hydrophobic |
| C24 | CG1 | ILE- 174 | 3.8 | 0 | Hydrophobic |
| C7 | OD2 | ASP- 189 | 3.52 | 0 | Ionic (Ligand Cationic) |
| C7 | OD1 | ASP- 189 | 3.85 | 0 | Ionic (Ligand Cationic) |
| N9 | OD1 | ASP- 189 | 3.12 | 149.5 | H-Bond (Ligand Donor) |
| N8 | OD2 | ASP- 189 | 2.63 | 165.36 | H-Bond (Ligand Donor) |
| C11 | CB | SER- 195 | 3.94 | 0 | Hydrophobic |
| C3 | CB | SER- 195 | 3.94 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 213 | 3.84 | 0 | Hydrophobic |
| C18 | CB | TRP- 215 | 3.85 | 0 | Hydrophobic |
| C25 | CB | TRP- 215 | 4.44 | 0 | Hydrophobic |
| C30 | CZ3 | TRP- 215 | 3.96 | 0 | Hydrophobic |
| C14 | CB | TRP- 215 | 3.87 | 0 | Hydrophobic |
| C24 | CE3 | TRP- 215 | 3.39 | 0 | Hydrophobic |
| N16 | N | GLY- 216 | 3.43 | 155.23 | H-Bond (Protein Donor) |
| C30 | CG | GLU- 217 | 3.5 | 0 | Hydrophobic |
| N8 | O | GLY- 219 | 3.1 | 132.61 | H-Bond (Ligand Donor) |
| C6 | SG | CYS- 220 | 4.34 | 0 | Hydrophobic |
