sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.790 Å
X-ray
2006-02-17
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.820 | 7.820 | 7.820 | 0.000 | 7.820 | 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: | 17.898 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.850 | 783.000 |
| % Hydrophobic | % Polar |
|---|---|
| 41.81 | 58.19 |
| According to VolSite | |
| HET Code: | 348 |
|---|---|
| Formula: | C27H36N4O2 |
| Molecular weight: | 448.600 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.27 % |
| Polar Surface area: | 85.58 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 17.0632 | -12.4527 | 21.7582 |
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 |
| C41 | CB | HIS- 57 | 4.05 | 0 | Hydrophobic |
| C42 | CB | HIS- 57 | 3.71 | 0 | Hydrophobic |
| C18 | CZ | TYR- 60 | 4.3 | 0 | Hydrophobic |
| C41 | CD2 | TYR- 60 | 3.58 | 0 | Hydrophobic |
| C42 | CE1 | TYR- 60 | 4.45 | 0 | Hydrophobic |
| C14 | CZ3 | TRP- 60 | 4.43 | 0 | Hydrophobic |
| C18 | CH2 | TRP- 60 | 4.27 | 0 | Hydrophobic |
| C41 | CZ3 | TRP- 60 | 3.91 | 0 | Hydrophobic |
| C28 | CB | LEU- 99 | 3.95 | 0 | Hydrophobic |
| C42 | CD2 | LEU- 99 | 3.34 | 0 | Hydrophobic |
| C31 | CD2 | LEU- 99 | 4.45 | 0 | Hydrophobic |
| C28 | CG2 | ILE- 174 | 3.72 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 189 | 2.82 | 166.52 | H-Bond (Ligand Donor) |
| N2 | OD1 | ASP- 189 | 2.81 | 146.94 | H-Bond (Ligand Donor) |
| C3 | OD2 | ASP- 189 | 3.65 | 0 | Ionic (Ligand Cationic) |
| C3 | OD1 | ASP- 189 | 3.59 | 0 | Ionic (Ligand Cationic) |
| C13 | CG | GLU- 192 | 4.14 | 0 | Hydrophobic |
| C6 | CB | SER- 195 | 3.95 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 213 | 3.93 | 0 | Hydrophobic |
| C22 | CB | TRP- 215 | 4.39 | 0 | Hydrophobic |
| C28 | CD2 | TRP- 215 | 3.66 | 0 | Hydrophobic |
| C26 | CB | TRP- 215 | 3.78 | 0 | Hydrophobic |
| O21 | N | GLY- 216 | 2.99 | 166.17 | H-Bond (Protein Donor) |
| N1 | O | GLY- 219 | 2.88 | 143.16 | H-Bond (Ligand Donor) |
| C9 | SG | CYS- 220 | 4.42 | 0 | Hydrophobic |
