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
2008-09-10
| 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: | 14.235 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.396 | 425.250 |
| % Hydrophobic | % Polar |
|---|---|
| 44.44 | 55.56 |
| According to VolSite | |
| HET Code: | M18 |
|---|---|
| Formula: | C20H27ClN2O5 |
| Molecular weight: | 410.892 g/mol |
| DrugBank ID: | DB08152 |
| Buried Surface Area: | 60.67 % |
| Polar Surface area: | 84.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 16.7582 | -12.7676 | 22.3989 |
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 |
| C3 | CH2 | TRP- 60 | 3.75 | 0 | Hydrophobic |
| C5 | CH2 | TRP- 60 | 4.45 | 0 | Hydrophobic |
| C6 | CZ | TYR- 60 | 3.64 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 99 | 3.46 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 99 | 3.31 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 174 | 3.3 | 0 | Hydrophobic |
| CL1 | CB | ALA- 190 | 3.92 | 0 | Hydrophobic |
| C18 | CB | ALA- 190 | 3.67 | 0 | Hydrophobic |
| CL1 | CG1 | VAL- 213 | 3.75 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 213 | 3.7 | 0 | Hydrophobic |
| C14 | CB | TRP- 215 | 3.68 | 0 | Hydrophobic |
| C12 | CE3 | TRP- 215 | 3.28 | 0 | Hydrophobic |
| O1 | N | GLY- 216 | 2.86 | 159.81 | H-Bond (Protein Donor) |
| C19 | SG | CYS- 220 | 4.25 | 0 | Hydrophobic |
| CL1 | CZ | TYR- 228 | 3.82 | 0 | Hydrophobic |
