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: | 9.000 | 9.000 | 9.000 | 0.000 | 9.000 | 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 |
|---|---|
| B | 100 % |
| B-Factor: | 24.577 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.255 | 421.875 |
| % Hydrophobic | % Polar |
|---|---|
| 38.40 | 61.60 |
| According to VolSite | |
| HET Code: | CDB |
|---|---|
| Formula: | C21H21F3N6O2 |
| Molecular weight: | 446.426 g/mol |
| DrugBank ID: | DB07549 |
| Buried Surface Area: | 61.47 % |
| Polar Surface area: | 99.57 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 16.9586 | -13.7838 | 23.26 |
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 |
| C29 | CB | HIS- 57 | 4.24 | 0 | Hydrophobic |
| C29 | CZ | TYR- 60 | 4.06 | 0 | Hydrophobic |
| C29 | CZ3 | TRP- 60 | 3.96 | 0 | Hydrophobic |
| C29 | CD1 | LEU- 99 | 4.09 | 0 | Hydrophobic |
| C33 | CD1 | LEU- 99 | 4.17 | 0 | Hydrophobic |
| C4 | CG | LEU- 99 | 3.66 | 0 | Hydrophobic |
| C3 | CG1 | ILE- 174 | 4.4 | 0 | Hydrophobic |
| F13 | CG1 | ILE- 174 | 4.19 | 0 | Hydrophobic |
| F1 | CD1 | ILE- 174 | 3.9 | 0 | Hydrophobic |
| C1 | CB | ALA- 190 | 4.01 | 0 | Hydrophobic |
| C44 | CB | ALA- 190 | 3.98 | 0 | Hydrophobic |
| F47 | CB | VAL- 213 | 4.42 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 213 | 3.82 | 0 | Hydrophobic |
| N37 | O | SER- 214 | 3.29 | 154.07 | H-Bond (Ligand Donor) |
| C3 | CB | TRP- 215 | 4.33 | 0 | Hydrophobic |
| C33 | CB | TRP- 215 | 3.98 | 0 | Hydrophobic |
| F13 | CE3 | TRP- 215 | 3.36 | 0 | Hydrophobic |
| N18 | O | GLY- 216 | 3.19 | 174.37 | H-Bond (Ligand Donor) |
| O28 | N | GLY- 216 | 3.12 | 163.75 | H-Bond (Protein Donor) |
| F13 | CG | GLU- 217 | 3.38 | 0 | Hydrophobic |
