sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.990 Å
X-ray
2002-09-23
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.380 | 8.380 | 8.380 | 0.000 | 8.380 | 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: | 21.898 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.598 | 637.875 |
| % Hydrophobic | % Polar |
|---|---|
| 38.62 | 61.38 |
| According to VolSite | |
| HET Code: | CDA |
|---|---|
| Formula: | C20H19F3N6O2 |
| Molecular weight: | 432.399 g/mol |
| DrugBank ID: | DB07548 |
| Buried Surface Area: | 59.78 % |
| Polar Surface area: | 99.57 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 17.0317 | -13.907 | 23.093 |
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 |
| C29 | CB | HIS- 57 | 4.2 | 0 | Hydrophobic |
| C29 | CE2 | TYR- 60 | 3.94 | 0 | Hydrophobic |
| C29 | CZ3 | TRP- 60 | 3.95 | 0 | Hydrophobic |
| C29 | CD1 | LEU- 99 | 4.17 | 0 | Hydrophobic |
| C33 | CD1 | LEU- 99 | 4.07 | 0 | Hydrophobic |
| C4 | CG | LEU- 99 | 3.68 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 174 | 4.27 | 0 | Hydrophobic |
| F13 | CG1 | ILE- 174 | 4.39 | 0 | Hydrophobic |
| F1 | CD1 | ILE- 174 | 3.84 | 0 | Hydrophobic |
| C45 | CB | ALA- 190 | 4.01 | 0 | Hydrophobic |
| N37 | O | SER- 214 | 3.11 | 160.79 | H-Bond (Ligand Donor) |
| C3 | CB | TRP- 215 | 4.28 | 0 | Hydrophobic |
| C33 | CB | TRP- 215 | 4.04 | 0 | Hydrophobic |
| F13 | CE3 | TRP- 215 | 3.32 | 0 | Hydrophobic |
| N18 | O | GLY- 216 | 3.18 | 170.98 | H-Bond (Ligand Donor) |
| O28 | N | GLY- 216 | 3.07 | 162.42 | H-Bond (Protein Donor) |
| F13 | CG | GLU- 217 | 3.41 | 0 | Hydrophobic |
| F47 | SG | CYS- 220 | 3.89 | 0 | Hydrophobic |
