sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2012-10-05
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.410 | 7.990 | 8.000 | 0.370 | 8.620 | 9 |
| 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 |
|---|---|
| D | 100 % |
| B-Factor: | 59.105 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.744 | 847.125 |
| % Hydrophobic | % Polar |
|---|---|
| 37.05 | 62.95 |
| According to VolSite | |
| HET Code: | 15U |
|---|---|
| Formula: | C23H36N6O5S |
| Molecular weight: | 508.634 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.52 % |
| Polar Surface area: | 190.65 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| 53.5638 | -31.7591 | -6.40763 |
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 |
| C71 | CB | HIS- 57 | 4.44 | 0 | Hydrophobic |
| C21 | CH2 | TRP- 60 | 3.38 | 0 | Hydrophobic |
| C71 | CZ3 | TRP- 60 | 4.26 | 0 | Hydrophobic |
| C71 | CZ | TYR- 60 | 3.67 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 99 | 4.44 | 0 | Hydrophobic |
| C41 | CD2 | LEU- 99 | 3.95 | 0 | Hydrophobic |
| C1 | CD1 | ILE- 174 | 4.11 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 174 | 3.87 | 0 | Hydrophobic |
| NH1 | OD1 | ASP- 189 | 3.37 | 142.03 | H-Bond (Ligand Donor) |
| NE | O | ALA- 190 | 3.3 | 134.35 | H-Bond (Ligand Donor) |
| C10 | CE3 | TRP- 215 | 3.57 | 0 | Hydrophobic |
| N1 | O | GLY- 216 | 3.08 | 147.65 | H-Bond (Ligand Donor) |
| O | N | GLY- 216 | 3.18 | 154.25 | H-Bond (Protein Donor) |
| C1 | CG | GLU- 217 | 4.22 | 0 | Hydrophobic |
