sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.670 Å
X-ray
2003-04-07
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.240 | 7.240 | 7.240 | 0.000 | 7.240 | 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: | 13.793 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.786 | 722.250 |
| % Hydrophobic | % Polar |
|---|---|
| 42.06 | 57.94 |
| According to VolSite | |
| HET Code: | FSN |
|---|---|
| Formula: | C23H25FN4O2 |
| Molecular weight: | 408.469 g/mol |
| DrugBank ID: | DB07796 |
| Buried Surface Area: | 60.86 % |
| Polar Surface area: | 93.43 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 16.7934 | -12.3784 | 21.8294 |
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 | CZ3 | TRP- 60 | 4.04 | 0 | Hydrophobic |
| F29 | CB | ASN- 98 | 4.14 | 0 | Hydrophobic |
| C25 | CD1 | LEU- 99 | 4 | 0 | Hydrophobic |
| C26 | CG | LEU- 99 | 3.67 | 0 | Hydrophobic |
| F29 | CD1 | ILE- 174 | 3.82 | 0 | Hydrophobic |
| C3 | OD2 | ASP- 189 | 3.63 | 0 | Ionic (Ligand Cationic) |
| C3 | OD1 | ASP- 189 | 3.68 | 0 | Ionic (Ligand Cationic) |
| N1 | OD2 | ASP- 189 | 2.78 | 172.97 | H-Bond (Ligand Donor) |
| N2 | OD1 | ASP- 189 | 2.81 | 153.13 | H-Bond (Ligand Donor) |
| C13 | CG | GLU- 192 | 4.31 | 0 | Hydrophobic |
| C6 | CB | SER- 195 | 3.85 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 213 | 3.82 | 0 | Hydrophobic |
| C22 | CB | TRP- 215 | 4.16 | 0 | Hydrophobic |
| C32 | CB | TRP- 215 | 3.75 | 0 | Hydrophobic |
| O21 | N | GLY- 216 | 3.07 | 158.7 | H-Bond (Protein Donor) |
| N1 | O | GLY- 219 | 2.88 | 136.23 | H-Bond (Ligand Donor) |
