sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.180 Å
X-ray
2008-01-24
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.920 | 8.920 | 8.920 | 0.000 | 8.920 | 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: | 23.311 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.865 | 330.750 |
| % Hydrophobic | % Polar |
|---|---|
| 47.96 | 52.04 |
| According to VolSite | |
| HET Code: | DKK |
|---|---|
| Formula: | C19H21F3N7O2 |
| Molecular weight: | 436.411 g/mol |
| DrugBank ID: | DB07665 |
| Buried Surface Area: | 64.3 % |
| Polar Surface area: | 150.67 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 5 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 17.2891 | -14.0331 | 23.1915 |
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 |
| C12 | CD1 | LEU- 132 | 4.05 | 0 | Hydrophobic |
| C29 | CG | LEU- 132 | 3.84 | 0 | Hydrophobic |
| F24 | CG1 | ILE- 209 | 4.13 | 0 | Hydrophobic |
| C31 | CD1 | ILE- 209 | 3.97 | 0 | Hydrophobic |
| F25 | CD1 | ILE- 209 | 3.79 | 0 | Hydrophobic |
| N3 | OD2 | ASP- 229 | 2.73 | 151.53 | H-Bond (Ligand Donor) |
| N3 | OD1 | ASP- 229 | 3.49 | 125.24 | H-Bond (Ligand Donor) |
| C6 | CG1 | VAL- 255 | 3.69 | 0 | Hydrophobic |
| N8 | O | SER- 256 | 2.9 | 167.51 | H-Bond (Ligand Donor) |
| C31 | CE3 | TRP- 257 | 3.42 | 0 | Hydrophobic |
| C12 | CB | TRP- 257 | 4.09 | 0 | Hydrophobic |
| C17 | CB | TRP- 257 | 3.63 | 0 | Hydrophobic |
| C31 | CB | TRP- 257 | 4.22 | 0 | Hydrophobic |
| F24 | CE3 | TRP- 257 | 3.27 | 0 | Hydrophobic |
| N21 | O | GLY- 258 | 2.81 | 178.53 | H-Bond (Ligand Donor) |
| F24 | CG | GLU- 259 | 3.27 | 0 | Hydrophobic |
| N3 | O | GLY- 260 | 2.77 | 154.04 | H-Bond (Ligand Donor) |
| N20 | O | HOH- 5039 | 2.76 | 165.56 | H-Bond (Protein Donor) |
| N4 | O | HOH- 5044 | 2.8 | 149.05 | H-Bond (Ligand Donor) |
