sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2011-01-19
| 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 |
|---|---|
| D | 100 % |
| B-Factor: | 88.813 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.639 | 475.875 |
| % Hydrophobic | % Polar |
|---|---|
| 49.65 | 50.35 |
| According to VolSite | |
| HET Code: | PRO_ALA_PRO_ARG |
|---|---|
| Formula: | C19H34N7O5 |
| Molecular weight: | 440.517 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 53.31 % |
| Polar Surface area: | 201.25 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 6 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| -6.62458 | -12.6484 | 36.2599 |
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 |
| CB | CB | HIS- 57 | 4.29 | 0 | Hydrophobic |
| N | NE2 | HIS- 57 | 3.27 | 126.12 | H-Bond (Ligand Donor) |
| CG | CE2 | TYR- 60 | 4.07 | 0 | Hydrophobic |
| CG | CH2 | TRP- 60 | 3.26 | 0 | Hydrophobic |
| CB | CD1 | LEU- 99 | 4.4 | 0 | Hydrophobic |
| CB | CD2 | LEU- 99 | 3.44 | 0 | Hydrophobic |
| CG | CD1 | ILE- 174 | 3.46 | 0 | Hydrophobic |
| CZ | OD2 | ASP- 189 | 3.48 | 0 | Ionic (Ligand Cationic) |
| CD | CB | ALA- 190 | 4.28 | 0 | Hydrophobic |
| O | N | GLY- 193 | 2.69 | 149.33 | H-Bond (Protein Donor) |
| CB | CB | SER- 195 | 3.33 | 0 | Hydrophobic |
| CB | CG1 | VAL- 213 | 4.47 | 0 | Hydrophobic |
| CD | CG1 | VAL- 213 | 3.81 | 0 | Hydrophobic |
| O | N | GLY- 216 | 3.48 | 146.81 | H-Bond (Protein Donor) |
| NH2 | O | GLY- 219 | 3.23 | 145.44 | H-Bond (Ligand Donor) |
