sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
1999-10-05
| 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 |
|---|---|
| 2 | 100 % |
| B-Factor: | 15.751 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.014 | 887.625 |
| % Hydrophobic | % Polar |
|---|---|
| 42.97 | 57.03 |
| According to VolSite | |
| HET Code: | IH3 |
|---|---|
| Formula: | C31H36N7O3 |
| Molecular weight: | 554.663 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.4 % |
| Polar Surface area: | 128.91 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 4 |
| Rings: | 6 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 30.8212 | 48.7267 | -2.56385 |
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 |
| C15 | CB | HIS- 57 | 4.01 | 0 | Hydrophobic |
| C16 | CE2 | TYR- 60 | 3.4 | 0 | Hydrophobic |
| C15 | CG | TYR- 60 | 3.71 | 0 | Hydrophobic |
| C16 | CH2 | TRP- 60 | 3.32 | 0 | Hydrophobic |
| C15 | CZ3 | TRP- 60 | 3.63 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 99 | 4.42 | 0 | Hydrophobic |
| C25 | CD1 | LEU- 99 | 4.36 | 0 | Hydrophobic |
| C26 | CG | LEU- 99 | 3.67 | 0 | Hydrophobic |
| C31 | CG1 | ILE- 174 | 4.36 | 0 | Hydrophobic |
| C33 | CD1 | ILE- 174 | 3.34 | 0 | Hydrophobic |
| C30 | CD1 | ILE- 174 | 3.41 | 0 | Hydrophobic |
| NA | OD2 | ASP- 189 | 2.87 | 163.32 | H-Bond (Ligand Donor) |
| C7 | CB | GLU- 192 | 4.33 | 0 | Hydrophobic |
| C25 | CB | TRP- 215 | 3.89 | 0 | Hydrophobic |
| C32 | CG | GLU- 217 | 3.43 | 0 | Hydrophobic |
