sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2008-01-28
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.750 | 6.890 | 6.960 | 0.100 | 6.960 | 3 |
| 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: | 17.579 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.910 | 465.750 |
| % Hydrophobic | % Polar |
|---|---|
| 49.28 | 50.72 |
| According to VolSite | |
| HET Code: | 29U |
|---|---|
| Formula: | C17H27N5O2 |
| Molecular weight: | 333.429 g/mol |
| DrugBank ID: | DB06947 |
| Buried Surface Area: | 59.23 % |
| Polar Surface area: | 128.66 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 15.6299 | -12.2316 | 22.0442 |
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 | CH2 | TRP- 60 | 3.99 | 0 | Hydrophobic |
| C3 | CZ | TYR- 60 | 3.4 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 99 | 3.91 | 0 | Hydrophobic |
| C48 | CD1 | ILE- 174 | 3.62 | 0 | Hydrophobic |
| C21 | OD2 | ASP- 189 | 3.61 | 0 | Ionic (Ligand Cationic) |
| C21 | OD1 | ASP- 189 | 3.53 | 0 | Ionic (Ligand Cationic) |
| N46 | OD2 | ASP- 189 | 2.82 | 160.67 | H-Bond (Ligand Donor) |
| N47 | OD1 | ASP- 189 | 2.79 | 143.39 | H-Bond (Ligand Donor) |
| C27 | CB | ALA- 190 | 4.2 | 0 | Hydrophobic |
| C27 | CG1 | VAL- 213 | 3.65 | 0 | Hydrophobic |
| N23 | O | SER- 214 | 2.93 | 161.37 | H-Bond (Ligand Donor) |
| C48 | CE3 | TRP- 215 | 3.73 | 0 | Hydrophobic |
| N13 | O | GLY- 216 | 2.78 | 173.36 | H-Bond (Ligand Donor) |
| O32 | N | GLY- 216 | 3.18 | 167.39 | H-Bond (Protein Donor) |
| C33 | CG | GLU- 217 | 4.34 | 0 | Hydrophobic |
| N46 | O | GLY- 219 | 2.91 | 135.06 | H-Bond (Ligand Donor) |
