sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2007-12-01
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.250 | 4.250 | 4.250 | 0.000 | 4.250 | 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: | 20.850 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.585 | 334.125 |
| % Hydrophobic | % Polar |
|---|---|
| 47.47 | 52.53 |
| According to VolSite | |
| HET Code: | 11U |
|---|---|
| Formula: | C21H33N5O2 |
| Molecular weight: | 387.519 g/mol |
| DrugBank ID: | DB06850 |
| Buried Surface Area: | 59.15 % |
| Polar Surface area: | 117.63 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 15.5949 | -11.8846 | 21.7563 |
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 |
| C3 | CB | HIS- 57 | 4.13 | 0 | Hydrophobic |
| C4 | CE2 | TYR- 60 | 3.65 | 0 | Hydrophobic |
| C4 | CH2 | TRP- 60 | 3.64 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 99 | 3.73 | 0 | Hydrophobic |
| C31 | OD1 | ASP- 189 | 3.61 | 0 | Ionic (Ligand Cationic) |
| C31 | OD2 | ASP- 189 | 3.56 | 0 | Ionic (Ligand Cationic) |
| N49 | OD2 | ASP- 189 | 2.77 | 154.46 | H-Bond (Ligand Donor) |
| N48 | OD1 | ASP- 189 | 2.65 | 145.67 | H-Bond (Ligand Donor) |
| N48 | OD2 | ASP- 189 | 3.47 | 125.8 | H-Bond (Ligand Donor) |
| C27 | CB | ALA- 190 | 4.28 | 0 | Hydrophobic |
| C27 | CG1 | VAL- 213 | 3.72 | 0 | Hydrophobic |
| N23 | O | SER- 214 | 3.01 | 164.73 | H-Bond (Ligand Donor) |
| N49 | O | GLY- 219 | 2.92 | 142.02 | H-Bond (Ligand Donor) |
| C29 | SG | CYS- 220 | 4.42 | 0 | Hydrophobic |
