sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.540 Å
X-ray
2004-05-24
| 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: | 14.539 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.902 | 486.000 |
| % Hydrophobic | % Polar |
|---|---|
| 50.00 | 50.00 |
| According to VolSite | |
| HET Code: | SHY |
|---|---|
| Formula: | C24H26N4O5 |
| Molecular weight: | 450.487 g/mol |
| DrugBank ID: | DB08546 |
| Buried Surface Area: | 61.28 % |
| Polar Surface area: | 132.11 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 4 |
| Rings: | 6 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 17.3758 | -12.3676 | 21.6712 |
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 |
| O27 | OH | TYR- 60 | 3.16 | 137.25 | H-Bond (Protein Donor) |
| C14 | CZ3 | TRP- 60 | 4.22 | 0 | Hydrophobic |
| C28 | CG | LEU- 99 | 3.73 | 0 | Hydrophobic |
| C26 | CG | LEU- 99 | 3.64 | 0 | Hydrophobic |
| C25 | CD1 | LEU- 99 | 4.07 | 0 | Hydrophobic |
| C31 | CD1 | ILE- 174 | 4.38 | 0 | Hydrophobic |
| N1 | OD1 | ASP- 189 | 2.9 | 144.6 | H-Bond (Ligand Donor) |
| N2 | OD2 | ASP- 189 | 2.82 | 162.49 | H-Bond (Ligand Donor) |
| C3 | OD2 | ASP- 189 | 3.69 | 0 | Ionic (Ligand Cationic) |
| C3 | OD1 | ASP- 189 | 3.71 | 0 | Ionic (Ligand Cationic) |
| C8 | CB | SER- 195 | 3.85 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 213 | 3.82 | 0 | Hydrophobic |
| C22 | CB | TRP- 215 | 4.13 | 0 | Hydrophobic |
| C32 | CB | TRP- 215 | 3.76 | 0 | Hydrophobic |
| O21 | N | GLY- 216 | 3.04 | 158.22 | H-Bond (Protein Donor) |
| N2 | O | GLY- 219 | 2.8 | 133.27 | H-Bond (Ligand Donor) |
| C5 | SG | CYS- 220 | 4.47 | 0 | Hydrophobic |
