sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2007-08-27
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.330 | 7.330 | 7.330 | 0.000 | 7.330 | 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 |
|---|---|
| B | 100 % |
| B-Factor: | 25.196 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.891 | 563.625 |
| % Hydrophobic | % Polar |
|---|---|
| 45.51 | 54.49 |
| According to VolSite | |
| HET Code: | I50 |
|---|---|
| Formula: | C19H22ClF3N5O2 |
| Molecular weight: | 444.858 g/mol |
| DrugBank ID: | DB07946 |
| Buried Surface Area: | 62.21 % |
| Polar Surface area: | 114 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 5 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 17.103 | -14.1565 | 23.3845 |
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 |
| CL18 | CB | HIS- 79 | 4.18 | 0 | Hydrophobic |
| CL18 | CE2 | TYR- 83 | 3.71 | 0 | Hydrophobic |
| CL18 | CZ3 | TRP- 86 | 3.82 | 0 | Hydrophobic |
| CL18 | CD1 | LEU- 132 | 3.99 | 0 | Hydrophobic |
| C28 | CG | LEU- 132 | 3.94 | 0 | Hydrophobic |
| C29 | CD1 | LEU- 132 | 3.93 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 132 | 4.03 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 132 | 3.81 | 0 | Hydrophobic |
| F31 | CG1 | ILE- 209 | 4.11 | 0 | Hydrophobic |
| F32 | CD1 | ILE- 209 | 3.9 | 0 | Hydrophobic |
| C25 | CD1 | ILE- 209 | 3.98 | 0 | Hydrophobic |
| N3 | OD2 | ASP- 229 | 2.75 | 175.27 | H-Bond (Ligand Donor) |
| C6 | CG1 | VAL- 255 | 3.73 | 0 | Hydrophobic |
| N8 | O | SER- 256 | 3.05 | 154.36 | H-Bond (Ligand Donor) |
| F31 | CE3 | TRP- 257 | 3.52 | 0 | Hydrophobic |
| C30 | CB | TRP- 257 | 4.3 | 0 | Hydrophobic |
| F19 | CB | TRP- 257 | 3.39 | 0 | Hydrophobic |
| N20 | O | GLY- 258 | 2.94 | 173.06 | H-Bond (Ligand Donor) |
| F31 | CG | GLU- 259 | 3.2 | 0 | Hydrophobic |
| N3 | O | GLY- 260 | 2.79 | 144.69 | H-Bond (Ligand Donor) |
