sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.650 Å
X-ray
2004-09-02
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.720 | 5.720 | 5.720 | 0.000 | 5.720 | 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: | 14.769 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.214 | 614.250 |
| % Hydrophobic | % Polar |
|---|---|
| 37.36 | 62.64 |
| According to VolSite | |
| HET Code: | MIU |
|---|---|
| Formula: | C20H35F3N7O3S |
| Molecular weight: | 510.597 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.88 % |
| Polar Surface area: | 172.95 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 6 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 3 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| 16.778 | -14.5759 | 21.2281 |
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 |
| C8 | CB | HIS- 57 | 4.39 | 0 | Hydrophobic |
| C8 | CD | LYS- 60 | 3.77 | 0 | Hydrophobic |
| C33 | CD2 | TYR- 60 | 3.32 | 0 | Hydrophobic |
| C8 | CB | TYR- 60 | 3.79 | 0 | Hydrophobic |
| C33 | CE3 | TRP- 60 | 3.47 | 0 | Hydrophobic |
| F1 | CD1 | LEU- 99 | 3.46 | 0 | Hydrophobic |
| F6 | CD1 | ILE- 174 | 3.68 | 0 | Hydrophobic |
| N19 | O | ALA- 190 | 3.22 | 159.85 | H-Bond (Ligand Donor) |
| F1 | CB | TRP- 215 | 4.06 | 0 | Hydrophobic |
| F6 | CE3 | TRP- 215 | 3.28 | 0 | Hydrophobic |
| N22 | O | TRP- 215 | 3.33 | 126.41 | H-Bond (Ligand Donor) |
| N21 | O | TRP- 215 | 3.46 | 124.32 | H-Bond (Ligand Donor) |
| N12 | O | GLY- 216 | 2.73 | 152.42 | H-Bond (Ligand Donor) |
| O15 | N | GLY- 216 | 3.01 | 157.61 | H-Bond (Protein Donor) |
| O24 | N | GLY- 219 | 3.21 | 152.24 | H-Bond (Protein Donor) |
| C17 | SG | CYS- 220 | 4.23 | 0 | Hydrophobic |
| N22 | O | HOH- 2121 | 3.12 | 138.83 | H-Bond (Ligand Donor) |
| N21 | O | HOH- 2125 | 2.92 | 136.91 | H-Bond (Ligand Donor) |
