sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2007-02-20
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.440 | 6.440 | 6.440 | 0.000 | 6.440 | 2 |
| 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 |
|---|---|
| D | 100 % |
| B-Factor: | 30.574 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.431 | 675.000 |
| % Hydrophobic | % Polar |
|---|---|
| 39.50 | 60.50 |
| According to VolSite | |
| HET Code: | 895 |
|---|---|
| Formula: | C17H22ClN3O5S2 |
| Molecular weight: | 447.957 g/mol |
| DrugBank ID: | DB07278 |
| Buried Surface Area: | 61.97 % |
| Polar Surface area: | 132.63 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 6.32479 | 19.856 | 49.3614 |
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 |
| C13 | CH2 | TRP- 60 | 4.49 | 0 | Hydrophobic |
| C20 | CZ3 | TRP- 60 | 3.72 | 0 | Hydrophobic |
| C22 | CZ3 | TRP- 60 | 4.01 | 0 | Hydrophobic |
| C20 | CE2 | TYR- 60 | 3.34 | 0 | Hydrophobic |
| CL1 | CB | ALA- 190 | 3.96 | 0 | Hydrophobic |
| S6 | CB | ALA- 190 | 4.27 | 0 | Hydrophobic |
| CL1 | CG1 | VAL- 213 | 3.5 | 0 | Hydrophobic |
| S6 | CG1 | VAL- 213 | 3.74 | 0 | Hydrophobic |
| C17 | CB | TRP- 215 | 4.01 | 0 | Hydrophobic |
| O3 | N | GLY- 216 | 2.94 | 149.64 | H-Bond (Protein Donor) |
| O1 | N | GLY- 219 | 3.39 | 128.8 | H-Bond (Protein Donor) |
| CL1 | CZ | TYR- 228 | 3.76 | 0 | Hydrophobic |
