sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.430 Å
X-ray
2010-09-30
| 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: | 15.508 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.782 | 364.500 |
| % Hydrophobic | % Polar |
|---|---|
| 50.00 | 50.00 |
| According to VolSite | |
| HET Code: | 99P |
|---|---|
| Formula: | C20H25N4O2 |
| Molecular weight: | 353.438 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.39 % |
| Polar Surface area: | 89.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| 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 |
|---|---|---|
| 17.2108 | -12.3728 | 22.3617 |
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 |
| C19 | CB | HIS- 57 | 4.49 | 0 | Hydrophobic |
| C20 | CH2 | TRP- 60 | 3.88 | 0 | Hydrophobic |
| C20 | CZ | TYR- 60 | 3.53 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 99 | 4.12 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 99 | 4.01 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 99 | 4.07 | 0 | Hydrophobic |
| C1 | CD1 | ILE- 174 | 4.02 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 174 | 3.8 | 0 | Hydrophobic |
| C26 | CG | GLU- 192 | 4.13 | 0 | Hydrophobic |
| N16 | O | SER- 214 | 2.8 | 173.79 | H-Bond (Ligand Donor) |
| C2 | CE3 | TRP- 215 | 4.39 | 0 | Hydrophobic |
| C12 | CB | TRP- 215 | 3.76 | 0 | Hydrophobic |
| N4 | O | GLY- 216 | 2.83 | 176.8 | H-Bond (Ligand Donor) |
| O7 | N | GLY- 216 | 3.01 | 163.21 | H-Bond (Protein Donor) |
| C2 | CG | GLU- 217 | 4.49 | 0 | Hydrophobic |
| C25 | SG | CYS- 220 | 4.18 | 0 | Hydrophobic |
