sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.750 Å
X-ray
2003-09-09
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.960 | 4.960 | 4.960 | 0.000 | 4.960 | 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: | 27.737 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.996 | 671.625 |
| % Hydrophobic | % Polar |
|---|---|
| 41.71 | 58.29 |
| According to VolSite | |
| HET Code: | CR9 |
|---|---|
| Formula: | C21H24FN4O2 |
| Molecular weight: | 383.439 g/mol |
| DrugBank ID: | DB03555 |
| Buried Surface Area: | 62.51 % |
| Polar Surface area: | 109.75 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 15.0623 | -12.3599 | 18.5733 |
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 |
| C2B | CG | LEU- 41 | 4.48 | 0 | Hydrophobic |
| C1A | CG | LEU- 41 | 4.44 | 0 | Hydrophobic |
| C1A | SG | CYS- 42 | 4.47 | 0 | Hydrophobic |
| C3B | CE2 | PHE- 60 | 4.34 | 0 | Hydrophobic |
| C3B | CG | LYS- 60 | 3.66 | 0 | Hydrophobic |
| C4B | CE3 | TRP- 60 | 4.31 | 0 | Hydrophobic |
| C6B | CZ3 | TRP- 60 | 4.07 | 0 | Hydrophobic |
| C4B | CB | TYR- 60 | 3.81 | 0 | Hydrophobic |
| C7 | OD2 | ASP- 189 | 3.66 | 0 | Ionic (Ligand Cationic) |
| C7 | OD1 | ASP- 189 | 3.76 | 0 | Ionic (Ligand Cationic) |
| N1 | OD2 | ASP- 189 | 2.96 | 149.32 | H-Bond (Ligand Donor) |
| N2 | OD2 | ASP- 189 | 3.49 | 130.21 | H-Bond (Ligand Donor) |
| N2 | OD1 | ASP- 189 | 2.91 | 137.41 | H-Bond (Ligand Donor) |
| F2 | CB | ALA- 190 | 3.5 | 0 | Hydrophobic |
| C2' | CG | GLU- 192 | 3.49 | 0 | Hydrophobic |
| C3 | CB | SER- 195 | 4.23 | 0 | Hydrophobic |
| C6' | CB | SER- 195 | 4.33 | 0 | Hydrophobic |
| F2 | CB | VAL- 213 | 4.35 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 213 | 3.75 | 0 | Hydrophobic |
| N1 | O | GLY- 219 | 2.71 | 124.5 | H-Bond (Ligand Donor) |
| C6 | SG | CYS- 220 | 4.31 | 0 | Hydrophobic |
| N3 | O | HOH- 445 | 2.73 | 160.45 | H-Bond (Protein Donor) |
