sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
1997-03-06
| 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: | 28.754 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.990 | 465.750 |
| % Hydrophobic | % Polar |
|---|---|
| 50.72 | 49.28 |
| According to VolSite | |
| HET Code: | AZL |
|---|---|
| Formula: | C21H34N5O4 |
| Molecular weight: | 420.526 g/mol |
| DrugBank ID: | DB07400 |
| Buried Surface Area: | 50.92 % |
| Polar Surface area: | 127.4 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| 17.3011 | -14.892 | 23.1922 |
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 |
| N7 | NE2 | HIS- 57 | 3.49 | 124.99 | H-Bond (Ligand Donor) |
| C11 | CH2 | TRP- 60 | 3.96 | 0 | Hydrophobic |
| C11 | CZ | TYR- 60 | 3.7 | 0 | Hydrophobic |
| C21 | CG | LEU- 99 | 3.71 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 99 | 3.64 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 174 | 3.63 | 0 | Hydrophobic |
| N1 | OD1 | ASP- 189 | 3.87 | 0 | Ionic (Ligand Cationic) |
| N1 | OD2 | ASP- 189 | 3.03 | 0 | Ionic (Ligand Cationic) |
| N1 | OD2 | ASP- 189 | 3.03 | 122.51 | H-Bond (Ligand Donor) |
| N6 | OG | SER- 195 | 2.8 | 158.05 | H-Bond (Ligand Donor) |
| C4 | CG1 | VAL- 213 | 4.48 | 0 | Hydrophobic |
| N7 | O | SER- 214 | 3.01 | 139.93 | H-Bond (Ligand Donor) |
| C16 | CE3 | TRP- 215 | 4.32 | 0 | Hydrophobic |
| C22 | CB | TRP- 215 | 3.76 | 0 | Hydrophobic |
| N9 | O | GLY- 216 | 3.21 | 165.98 | H-Bond (Ligand Donor) |
| O14 | N | GLY- 216 | 3.04 | 170.99 | H-Bond (Protein Donor) |
| N1 | O | GLY- 219 | 2.61 | 136.67 | H-Bond (Ligand Donor) |
