sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.580 Å
X-ray
2003-03-06
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.500 | 6.500 | 6.500 | 0.000 | 6.500 | 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: | 23.970 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.959 | 637.875 |
| % Hydrophobic | % Polar |
|---|---|
| 42.33 | 57.67 |
| According to VolSite | |
| HET Code: | 696 |
|---|---|
| Formula: | C21H18N3O |
| Molecular weight: | 328.387 g/mol |
| DrugBank ID: | DB03159 |
| Buried Surface Area: | 61.07 % |
| Polar Surface area: | 87.63 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 14.7461 | -12.2698 | 18.7896 |
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 |
| C3B | SG | CYS- 42 | 3.63 | 0 | Hydrophobic |
| C3B | CB | CYS- 58 | 4.36 | 0 | Hydrophobic |
| C5B | CB | TYR- 60 | 4.2 | 0 | Hydrophobic |
| C4B | CD | LYS- 60 | 4.46 | 0 | Hydrophobic |
| C5B | CG | LYS- 60 | 4.24 | 0 | Hydrophobic |
| C7 | OD2 | ASP- 189 | 3.87 | 0 | Ionic (Ligand Cationic) |
| C7 | OD1 | ASP- 189 | 3.83 | 0 | Ionic (Ligand Cationic) |
| N1 | OD2 | ASP- 189 | 3.13 | 155.19 | H-Bond (Ligand Donor) |
| N2 | OD1 | ASP- 189 | 3.08 | 137.35 | H-Bond (Ligand Donor) |
| C2 | CB | ALA- 190 | 4.01 | 0 | Hydrophobic |
| C3' | CG | GLU- 192 | 3.54 | 0 | Hydrophobic |
| C2' | CG | GLU- 192 | 3.57 | 0 | Hydrophobic |
| C6' | CB | SER- 195 | 4.35 | 0 | Hydrophobic |
| C3 | CB | SER- 195 | 4.25 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 213 | 3.5 | 0 | Hydrophobic |
