sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
1999-02-26
| 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: | 24.479 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.609 | 469.125 |
| % Hydrophobic | % Polar |
|---|---|
| 42.45 | 57.55 |
| According to VolSite | |
| HET Code: | ACE_0BN_CHG_PRR |
|---|---|
| Formula: | C27H41N6O3 |
| Molecular weight: | 497.653 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 55.68 % |
| Polar Surface area: | 161.55 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 6 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 3 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 15.6348 | -14.8576 | 22.5377 |
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 |
| C3 | CD1 | LEU- 99 | 3.8 | 0 | Hydrophobic |
| C4 | CG | GLU- 146 | 3.72 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 174 | 4.27 | 0 | Hydrophobic |
| N2 | OD1 | ASP- 189 | 3.07 | 142.61 | H-Bond (Ligand Donor) |
| N2 | OD2 | ASP- 189 | 3.06 | 156.53 | H-Bond (Ligand Donor) |
| N3 | OD1 | ASP- 189 | 3.02 | 148.01 | H-Bond (Ligand Donor) |
| C10 | OD1 | ASP- 189 | 3.48 | 0 | Ionic (Ligand Cationic) |
| C6 | CB | ALA- 190 | 4.38 | 0 | Hydrophobic |
| C5 | CB | GLU- 192 | 4.09 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 213 | 3.72 | 0 | Hydrophobic |
| C5 | CE3 | TRP- 215 | 4.44 | 0 | Hydrophobic |
| C4 | CB | TRP- 215 | 3.79 | 0 | Hydrophobic |
| O | N | GLY- 216 | 2.91 | 162.29 | H-Bond (Protein Donor) |
| N | O | GLY- 216 | 2.69 | 166.7 | H-Bond (Ligand Donor) |
| C5 | CG | GLU- 217 | 4.16 | 0 | Hydrophobic |
| C7 | SG | CYS- 220 | 4.14 | 0 | Hydrophobic |
| C4 | SG | CYS- 220 | 3.75 | 0 | Hydrophobic |
| N | O | HOH- 442 | 3.48 | 131.59 | H-Bond (Ligand Donor) |
