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
1999-10-15
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 23.974 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | NA |
| Ligandability | Volume (Å3) |
|---|---|
| 0.669 | 671.625 |
| % Hydrophobic | % Polar |
|---|---|
| 46.73 | 53.27 |
| According to VolSite | |
| HET Code: | 00R |
|---|---|
| Formula: | C24H30N7O5S |
| Molecular weight: | 528.604 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.56 % |
| Polar Surface area: | 171.42 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 16.8169 | -14.1756 | 23.1522 |
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 |
| C14 | CH2 | TRP- 60 | 3.81 | 0 | Hydrophobic |
| C14 | CZ | TYR- 60 | 3.37 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 99 | 4.34 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 99 | 3.71 | 0 | Hydrophobic |
| C39 | CG | LEU- 99 | 3.72 | 0 | Hydrophobic |
| C37 | CG1 | ILE- 174 | 4.18 | 0 | Hydrophobic |
| C41 | CD1 | ILE- 174 | 3.5 | 0 | Hydrophobic |
| N25 | OD2 | ASP- 189 | 3 | 131.63 | H-Bond (Ligand Donor) |
| N27 | OD1 | ASP- 189 | 2.77 | 120.42 | H-Bond (Ligand Donor) |
| N27 | OD2 | ASP- 189 | 3.5 | 120.44 | H-Bond (Ligand Donor) |
| C01 | CB | SER- 195 | 4.07 | 0 | Hydrophobic |
| C06 | CG1 | VAL- 213 | 3.76 | 0 | Hydrophobic |
| C17 | CB | TRP- 215 | 3.77 | 0 | Hydrophobic |
| C37 | CB | TRP- 215 | 4.46 | 0 | Hydrophobic |
| O13 | N | GLY- 216 | 3.08 | 162.67 | H-Bond (Protein Donor) |
| C04 | SG | CYS- 220 | 4.37 | 0 | Hydrophobic |
