sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2012-06-22
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.500 | 7.500 | 7.500 | 0.000 | 7.500 | 1 |
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 41.239 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.403 | 779.625 |
| % Hydrophobic | % Polar |
|---|---|
| 33.77 | 66.23 |
| According to VolSite | |
| HET Code: | 9MU |
|---|---|
| Formula: | C26H32N5O3S |
| Molecular weight: | 494.629 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 54.54 % |
| Polar Surface area: | 138.49 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 31.3061 | 13.6571 | 25.6789 |
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 |
| C5 | CD1 | LEU- 96 | 3.81 | 0 | Hydrophobic |
| C6 | CG | LEU- 96 | 3.84 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 179 | 4.23 | 0 | Hydrophobic |
| C33 | OD1 | ASP- 199 | 3.6 | 0 | Ionic (Ligand Cationic) |
| C33 | OD2 | ASP- 199 | 3.4 | 0 | Ionic (Ligand Cationic) |
| N34 | OD1 | ASP- 199 | 2.88 | 144.99 | H-Bond (Ligand Donor) |
| N35 | OD2 | ASP- 199 | 2.62 | 141.72 | H-Bond (Ligand Donor) |
| C31 | CB | ALA- 200 | 4.44 | 0 | Hydrophobic |
| C31 | CG1 | VAL- 225 | 3.97 | 0 | Hydrophobic |
| C3 | CB | TRP- 227 | 3.79 | 0 | Hydrophobic |
| O14 | N | GLY- 228 | 3.15 | 154.2 | H-Bond (Protein Donor) |
| O20 | N | GLY- 230 | 2.78 | 139.84 | H-Bond (Protein Donor) |
| N35 | O | GLY- 230 | 2.92 | 149.21 | H-Bond (Ligand Donor) |
| C26 | SG | CYS- 231 | 4.08 | 0 | Hydrophobic |
