sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.300 Å
X-ray
2006-02-17
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.100 | 8.100 | 8.100 | 0.000 | 8.100 | 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: | 22.508 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.796 | 779.625 |
| % Hydrophobic | % Polar |
|---|---|
| 41.99 | 58.01 |
| According to VolSite | |
| HET Code: | ESH |
|---|---|
| Formula: | C26H33ClN4O |
| Molecular weight: | 453.019 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.45 % |
| Polar Surface area: | 76.35 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 17.0029 | -12.4417 | 21.4792 |
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 |
| C41 | CB | HIS- 57 | 3.72 | 0 | Hydrophobic |
| C42 | CB | HIS- 57 | 4.06 | 0 | Hydrophobic |
| C18 | CH2 | TRP- 60 | 4.33 | 0 | Hydrophobic |
| C42 | CZ3 | TRP- 60 | 3.82 | 0 | Hydrophobic |
| C18 | CE2 | TYR- 60 | 4.14 | 0 | Hydrophobic |
| C41 | CE1 | TYR- 60 | 4.37 | 0 | Hydrophobic |
| C42 | CD2 | TYR- 60 | 3.57 | 0 | Hydrophobic |
| C31 | CD1 | LEU- 99 | 4.27 | 0 | Hydrophobic |
| C41 | CD2 | LEU- 99 | 3.88 | 0 | Hydrophobic |
| C30 | CG | LEU- 99 | 4.11 | 0 | Hydrophobic |
| CL30 | CD1 | ILE- 174 | 3.73 | 0 | Hydrophobic |
| N1 | OD1 | ASP- 189 | 2.89 | 146.62 | H-Bond (Ligand Donor) |
| N2 | OD2 | ASP- 189 | 2.79 | 160.99 | H-Bond (Ligand Donor) |
| C3 | OD2 | ASP- 189 | 3.69 | 0 | Ionic (Ligand Cationic) |
| C3 | OD1 | ASP- 189 | 3.62 | 0 | Ionic (Ligand Cationic) |
| C13 | CG | GLU- 192 | 4.15 | 0 | Hydrophobic |
| C8 | CB | SER- 195 | 3.9 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 213 | 3.84 | 0 | Hydrophobic |
| C22 | CB | TRP- 215 | 4.39 | 0 | Hydrophobic |
| C32 | CB | TRP- 215 | 3.87 | 0 | Hydrophobic |
| O21 | N | GLY- 216 | 3.03 | 166.53 | H-Bond (Protein Donor) |
| N2 | O | GLY- 219 | 2.89 | 148.18 | H-Bond (Ligand Donor) |
| C5 | SG | CYS- 220 | 4.42 | 0 | Hydrophobic |
