sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.960 Å
X-ray
2008-02-08
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.130 | 6.130 | 6.130 | 0.000 | 6.130 | 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: | 15.762 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.770 | 435.375 |
| % Hydrophobic | % Polar |
|---|---|
| 45.74 | 54.26 |
| According to VolSite | |
| HET Code: | 27U |
|---|---|
| Formula: | C22H27N4O2 |
| Molecular weight: | 379.475 g/mol |
| DrugBank ID: | DB06942 |
| Buried Surface Area: | 60.72 % |
| Polar Surface area: | 101.01 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 16.7216 | -12.5934 | 22.7442 |
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 |
| C6 | CB | HIS- 57 | 4.49 | 0 | Hydrophobic |
| C6 | CH2 | TRP- 60 | 4.07 | 0 | Hydrophobic |
| C5 | CZ | TYR- 60 | 3.43 | 0 | Hydrophobic |
| C20 | CD1 | LEU- 99 | 4.19 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 99 | 4.04 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 99 | 3.74 | 0 | Hydrophobic |
| C16 | OD1 | ASP- 189 | 3.52 | 0 | Ionic (Ligand Cationic) |
| C16 | OD2 | ASP- 189 | 3.48 | 0 | Ionic (Ligand Cationic) |
| N3 | OD2 | ASP- 189 | 2.7 | 148.92 | H-Bond (Ligand Donor) |
| N4 | OD1 | ASP- 189 | 2.72 | 156.4 | H-Bond (Ligand Donor) |
| N4 | OD2 | ASP- 189 | 3.49 | 122.04 | H-Bond (Ligand Donor) |
| C14 | CB | ALA- 190 | 4.35 | 0 | Hydrophobic |
| C14 | CG1 | VAL- 213 | 3.72 | 0 | Hydrophobic |
| N2 | O | SER- 214 | 2.92 | 172.7 | H-Bond (Ligand Donor) |
| C1 | CE3 | TRP- 215 | 4.33 | 0 | Hydrophobic |
| C22 | CB | TRP- 215 | 3.81 | 0 | Hydrophobic |
| O1 | N | GLY- 216 | 3.3 | 168.15 | H-Bond (Protein Donor) |
| C1 | CG | GLU- 217 | 4.46 | 0 | Hydrophobic |
| N4 | O | GLY- 219 | 3.04 | 142.19 | H-Bond (Ligand Donor) |
| C12 | SG | CYS- 220 | 4.36 | 0 | Hydrophobic |
