sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.980 Å
X-ray
2008-02-04
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.410 | 4.410 | 4.410 | 0.000 | 4.410 | 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 |
|---|---|
| H | 100 % |
| B-Factor: | 20.520 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.509 | 496.125 |
| % Hydrophobic | % Polar |
|---|---|
| 44.90 | 55.10 |
| According to VolSite | |
| HET Code: | 49U |
|---|---|
| Formula: | C21H31N4O2 |
| Molecular weight: | 371.496 g/mol |
| DrugBank ID: | DB07095 |
| Buried Surface Area: | 57.83 % |
| Polar Surface area: | 101.01 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 15.5054 | -11.9219 | 21.84 |
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 |
| C2 | CB | HIS- 57 | 4.34 | 0 | Hydrophobic |
| C3 | CH2 | TRP- 60 | 3.58 | 0 | Hydrophobic |
| C3 | CZ | TYR- 60 | 3.76 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 99 | 3.45 | 0 | Hydrophobic |
| C9 | OD2 | ASP- 189 | 3.59 | 0 | Ionic (Ligand Cationic) |
| C9 | OD1 | ASP- 189 | 3.32 | 0 | Ionic (Ligand Cationic) |
| N46 | OD2 | ASP- 189 | 2.73 | 153.83 | H-Bond (Ligand Donor) |
| N47 | OD1 | ASP- 189 | 2.61 | 136.77 | H-Bond (Ligand Donor) |
| C29 | CB | ALA- 190 | 4.21 | 0 | Hydrophobic |
| C29 | CG1 | VAL- 213 | 3.77 | 0 | Hydrophobic |
| N23 | O | SER- 214 | 3.12 | 155.56 | H-Bond (Ligand Donor) |
| C21 | CE3 | TRP- 215 | 3.99 | 0 | Hydrophobic |
| O32 | N | GLY- 216 | 3.05 | 166.08 | H-Bond (Protein Donor) |
| N46 | O | GLY- 219 | 3 | 145.94 | H-Bond (Ligand Donor) |
| C27 | SG | CYS- 220 | 4.34 | 0 | Hydrophobic |
