sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2004-02-09
| 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: | 20.408 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.647 | 465.750 |
| % Hydrophobic | % Polar |
|---|---|
| 47.10 | 52.90 |
| According to VolSite | |
| HET Code: | 165 |
|---|---|
| Formula: | C28H35N5O4S2 |
| Molecular weight: | 569.739 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.09 % |
| Polar Surface area: | 171.11 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 12.4341 | -14.7497 | 13.268 |
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 |
| O39 | NE2 | HIS- 57 | 3.06 | 124.56 | H-Bond (Protein Donor) |
| C21 | CE2 | TYR- 60 | 3.44 | 0 | Hydrophobic |
| C22 | CZ3 | TRP- 60 | 4.21 | 0 | Hydrophobic |
| C21 | CH2 | TRP- 60 | 4.31 | 0 | Hydrophobic |
| C16 | CG | LEU- 99 | 4.26 | 0 | Hydrophobic |
| C15 | CG | LEU- 99 | 4.28 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 174 | 4.44 | 0 | Hydrophobic |
| C17 | CD1 | ILE- 174 | 3.22 | 0 | Hydrophobic |
| N35 | OD2 | ASP- 189 | 3.11 | 136.15 | H-Bond (Ligand Donor) |
| S34 | CB | ALA- 190 | 3.81 | 0 | Hydrophobic |
| C27 | CB | GLU- 192 | 4.37 | 0 | Hydrophobic |
| S34 | CG1 | VAL- 213 | 3.77 | 0 | Hydrophobic |
| C12 | CB | TRP- 215 | 4.3 | 0 | Hydrophobic |
| C17 | CE3 | TRP- 215 | 3.42 | 0 | Hydrophobic |
| C16 | CD2 | TRP- 215 | 3.73 | 0 | Hydrophobic |
| C1 | CB | GLU- 217 | 3.77 | 0 | Hydrophobic |
| O36 | N | GLY- 219 | 3.29 | 164.57 | H-Bond (Protein Donor) |
| C28 | SG | CYS- 220 | 3.83 | 0 | Hydrophobic |
| O39 | O | HOH- 1083 | 3.25 | 139.05 | H-Bond (Protein Donor) |
