sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.860 Å
X-ray
2001-09-26
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.820 | 7.820 | 7.820 | 0.000 | 7.820 | 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: | 28.469 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.405 | 479.250 |
| % Hydrophobic | % Polar |
|---|---|
| 37.32 | 62.68 |
| According to VolSite | |
| HET Code: | IGN |
|---|---|
| Formula: | C21H39N6O4 |
| Molecular weight: | 439.572 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.88 % |
| Polar Surface area: | 169.79 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 5 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| 16.5054 | -13.1732 | 22.2186 |
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 |
| C14 | CB | HIS- 57 | 4.27 | 0 | Hydrophobic |
| C15 | CE2 | TYR- 60 | 3.42 | 0 | Hydrophobic |
| C15 | CH2 | TRP- 60 | 3.43 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 99 | 4.37 | 0 | Hydrophobic |
| C55 | CD1 | LEU- 99 | 3.81 | 0 | Hydrophobic |
| C54 | CD1 | ILE- 174 | 4.02 | 0 | Hydrophobic |
| C8 | OD1 | ASP- 189 | 3.46 | 0 | Ionic (Ligand Cationic) |
| C8 | OD2 | ASP- 189 | 3.62 | 0 | Ionic (Ligand Cationic) |
| N10 | OD2 | ASP- 189 | 2.85 | 130.54 | H-Bond (Ligand Donor) |
| C6 | CB | ALA- 190 | 4.07 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 213 | 3.75 | 0 | Hydrophobic |
| N3 | O | SER- 214 | 3 | 153.4 | H-Bond (Ligand Donor) |
| C34 | CE3 | TRP- 215 | 4.43 | 0 | Hydrophobic |
| C53 | CD2 | TRP- 215 | 3.63 | 0 | Hydrophobic |
| O31 | N | GLY- 216 | 3.02 | 164.66 | H-Bond (Protein Donor) |
| N21 | O | GLY- 216 | 2.93 | 164.6 | H-Bond (Ligand Donor) |
| N9 | O | GLY- 219 | 2.97 | 149.54 | H-Bond (Ligand Donor) |
| O24 | N | GLY- 219 | 2.76 | 177.89 | H-Bond (Protein Donor) |
