sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.750 Å
X-ray
2008-01-16
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.930 | 5.930 | 5.930 | 0.000 | 5.930 | 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: | 20.972 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.572 | 425.250 |
| % Hydrophobic | % Polar |
|---|---|
| 42.86 | 57.14 |
| According to VolSite | |
| HET Code: | 50U |
|---|---|
| Formula: | C22H33N4O2 |
| Molecular weight: | 385.523 g/mol |
| DrugBank ID: | DB07131 |
| Buried Surface Area: | 60.21 % |
| 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 |
|---|---|---|
| 16.6275 | -12.505 | 22.7165 |
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 | 4.31 | 0 | Hydrophobic |
| C3 | CZ | TYR- 60 | 3.48 | 0 | Hydrophobic |
| C46 | CB | LEU- 99 | 3.98 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 99 | 3.98 | 0 | Hydrophobic |
| C45 | CG1 | ILE- 174 | 4.49 | 0 | Hydrophobic |
| C21 | OD1 | ASP- 189 | 3.47 | 0 | Ionic (Ligand Cationic) |
| C21 | OD2 | ASP- 189 | 3.75 | 0 | Ionic (Ligand Cationic) |
| N46 | OD1 | ASP- 189 | 2.72 | 145.04 | H-Bond (Ligand Donor) |
| N47 | OD1 | ASP- 189 | 3.45 | 122.34 | H-Bond (Ligand Donor) |
| N47 | OD2 | ASP- 189 | 2.95 | 157.23 | H-Bond (Ligand Donor) |
| C29 | CB | ALA- 190 | 4.27 | 0 | Hydrophobic |
| C29 | CG1 | VAL- 213 | 3.69 | 0 | Hydrophobic |
| N23 | O | SER- 214 | 3 | 162.39 | H-Bond (Ligand Donor) |
| C44 | CB | TRP- 215 | 4.15 | 0 | Hydrophobic |
| C45 | CE3 | TRP- 215 | 3.29 | 0 | Hydrophobic |
| C46 | CD2 | TRP- 215 | 3.91 | 0 | Hydrophobic |
| C43 | CE3 | TRP- 215 | 4.08 | 0 | Hydrophobic |
| O32 | N | GLY- 216 | 3.28 | 167.39 | H-Bond (Protein Donor) |
| N47 | O | GLY- 219 | 2.99 | 145.96 | H-Bond (Ligand Donor) |
| C27 | SG | CYS- 220 | 4.46 | 0 | Hydrophobic |
