sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2002-09-23
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.640 | 8.640 | 8.640 | 0.000 | 8.640 | 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 |
|---|---|
| B | 100 % |
| B-Factor: | 22.517 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.780 | 479.250 |
| % Hydrophobic | % Polar |
|---|---|
| 45.77 | 54.23 |
| According to VolSite | |
| HET Code: | CDD |
|---|---|
| Formula: | C20H17ClF3N5O3 |
| Molecular weight: | 467.829 g/mol |
| DrugBank ID: | DB07550 |
| Buried Surface Area: | 61.18 % |
| Polar Surface area: | 99.26 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 17.1231 | -14.0414 | 23.2708 |
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 |
| CL43 | CB | HIS- 57 | 4.3 | 0 | Hydrophobic |
| CL43 | CZ | TYR- 60 | 3.74 | 0 | Hydrophobic |
| CL43 | CH2 | TRP- 60 | 3.97 | 0 | Hydrophobic |
| C24 | CD1 | LEU- 99 | 4.24 | 0 | Hydrophobic |
| CL43 | CD1 | LEU- 99 | 3.99 | 0 | Hydrophobic |
| C5 | CG | LEU- 99 | 3.81 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 174 | 4.43 | 0 | Hydrophobic |
| F14 | CG1 | ILE- 174 | 4.26 | 0 | Hydrophobic |
| F13 | CD1 | ILE- 174 | 3.83 | 0 | Hydrophobic |
| C34 | CB | ALA- 190 | 3.99 | 0 | Hydrophobic |
| C33 | CG1 | VAL- 213 | 3.69 | 0 | Hydrophobic |
| N28 | O | SER- 214 | 3.1 | 146.85 | H-Bond (Ligand Donor) |
| C11 | CE3 | TRP- 215 | 4.26 | 0 | Hydrophobic |
| F14 | CZ3 | TRP- 215 | 3.39 | 0 | Hydrophobic |
| C24 | CB | TRP- 215 | 4.08 | 0 | Hydrophobic |
| C4 | CE3 | TRP- 215 | 3.42 | 0 | Hydrophobic |
| C4 | CB | TRP- 215 | 4.12 | 0 | Hydrophobic |
| N15 | O | GLY- 216 | 2.63 | 175.33 | H-Bond (Ligand Donor) |
| O42 | N | GLY- 216 | 2.94 | 164.11 | H-Bond (Protein Donor) |
| F14 | CB | GLU- 217 | 4.38 | 0 | Hydrophobic |
| C11 | CG | GLU- 217 | 4.08 | 0 | Hydrophobic |
| C2 | SG | CYS- 220 | 4.19 | 0 | Hydrophobic |
| F1 | SG | CYS- 220 | 4.06 | 0 | Hydrophobic |
