sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.250 Å
X-ray
2008-01-08
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.890 | 5.030 | 5.030 | 0.140 | 5.170 | 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 |
|---|---|
| H | 100 % |
| B-Factor: | 19.968 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.765 | 415.125 |
| % Hydrophobic | % Polar |
|---|---|
| 43.90 | 56.10 |
| According to VolSite | |
| HET Code: | 19U |
|---|---|
| Formula: | C16H23ClN3O2 |
| Molecular weight: | 324.826 g/mol |
| DrugBank ID: | DB06878 |
| Buried Surface Area: | 59.33 % |
| Polar Surface area: | 77.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 15.8498 | -12.0353 | 22.087 |
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 | CZ3 | TRP- 60 | 4.03 | 0 | Hydrophobic |
| C3 | CH2 | TRP- 60 | 4.13 | 0 | Hydrophobic |
| C3 | CZ | TYR- 60 | 3.64 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 99 | 3.78 | 0 | Hydrophobic |
| CL21 | CB | ALA- 190 | 3.88 | 0 | Hydrophobic |
| C29 | CB | ALA- 190 | 3.85 | 0 | Hydrophobic |
| C30 | CG1 | VAL- 213 | 3.46 | 0 | Hydrophobic |
| N23 | O | SER- 214 | 2.6 | 166.43 | H-Bond (Ligand Donor) |
| C1 | CB | TRP- 215 | 4.15 | 0 | Hydrophobic |
| N | O | GLY- 216 | 2.86 | 163.34 | H-Bond (Ligand Donor) |
| O32 | N | GLY- 216 | 3.21 | 166.13 | H-Bond (Protein Donor) |
| C27 | SG | CYS- 220 | 4.17 | 0 | Hydrophobic |
| CL21 | CZ | TYR- 228 | 4.13 | 0 | Hydrophobic |
