sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2003-01-28
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.890 | 9.140 | 9.140 | 0.260 | 9.400 | 2 |
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 21.858 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.077 | 249.750 |
| % Hydrophobic | % Polar |
|---|---|
| 36.49 | 63.51 |
| According to VolSite | |
| HET Code: | T76 |
|---|---|
| Formula: | C25H33ClN4O5 |
| Molecular weight: | 505.006 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.85 % |
| Polar Surface area: | 116.83 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 15.8666 | -14.1447 | 22.5803 |
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 |
| C19 | CH2 | TRP- 60 | 3.89 | 0 | Hydrophobic |
| C19 | CE2 | TYR- 60 | 3.61 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 99 | 4.14 | 0 | Hydrophobic |
| C50 | CG | LEU- 99 | 4.33 | 0 | Hydrophobic |
| C51 | CD1 | LEU- 99 | 4.14 | 0 | Hydrophobic |
| C48 | CG1 | ILE- 174 | 3.85 | 0 | Hydrophobic |
| C49 | CD1 | ILE- 174 | 3.93 | 0 | Hydrophobic |
| CL68 | CB | ALA- 190 | 3.92 | 0 | Hydrophobic |
| C5 | CB | ALA- 190 | 3.95 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 213 | 3.54 | 0 | Hydrophobic |
| N8 | O | SER- 214 | 2.9 | 166.21 | H-Bond (Ligand Donor) |
| C51 | CB | TRP- 215 | 3.89 | 0 | Hydrophobic |
| C48 | CE3 | TRP- 215 | 3.81 | 0 | Hydrophobic |
| N31 | O | GLY- 216 | 2.82 | 126.79 | H-Bond (Ligand Donor) |
| O44 | N | GLY- 216 | 2.83 | 165.28 | H-Bond (Protein Donor) |
| C48 | CG | GLU- 217 | 4.28 | 0 | Hydrophobic |
| O42 | N | GLY- 219 | 2.98 | 129.95 | H-Bond (Protein Donor) |
| C43 | SG | CYS- 220 | 3.79 | 0 | Hydrophobic |
| CL68 | CZ | TYR- 228 | 4.11 | 0 | Hydrophobic |
