sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2004-05-19
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.130 | 9.130 | 9.130 | 0.000 | 9.130 | 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 |
|---|---|
| A | 100 % |
| B-Factor: | 29.392 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.929 | 857.250 |
| % Hydrophobic | % Polar |
|---|---|
| 41.34 | 58.66 |
| According to VolSite | |
| HET Code: | 177 |
|---|---|
| Formula: | C24H36ClN4O4 |
| Molecular weight: | 480.020 g/mol |
| DrugBank ID: | DB06869 |
| Buried Surface Area: | 61.15 % |
| Polar Surface area: | 115.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 15.3828 | -13.9895 | 22.4305 |
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 |
| CG | CZ | TYR- 60 | 3.66 | 0 | Hydrophobic |
| CB | CH2 | TRP- 60 | 3.94 | 0 | Hydrophobic |
| CG1 | CD1 | LEU- 99 | 4.26 | 0 | Hydrophobic |
| CD1 | CG | LEU- 99 | 4.29 | 0 | Hydrophobic |
| CG | CD1 | LEU- 99 | 4.09 | 0 | Hydrophobic |
| CN | CG | GLU- 146 | 3.32 | 0 | Hydrophobic |
| CE0 | CD1 | ILE- 174 | 4.14 | 0 | Hydrophobic |
| CD2 | CG1 | ILE- 174 | 3.95 | 0 | Hydrophobic |
| CL | CB | ALA- 190 | 4.04 | 0 | Hydrophobic |
| CDB | CB | ALA- 190 | 4 | 0 | Hydrophobic |
| CN | SG | CYS- 191 | 4.38 | 0 | Hydrophobic |
| CGB | CG1 | VAL- 213 | 3.6 | 0 | Hydrophobic |
| N' | O | SER- 214 | 2.99 | 165.79 | H-Bond (Ligand Donor) |
| CD1 | CD2 | TRP- 215 | 4.04 | 0 | Hydrophobic |
| CB0 | CB | TRP- 215 | 4.04 | 0 | Hydrophobic |
| CD2 | CE3 | TRP- 215 | 3.94 | 0 | Hydrophobic |
| N0 | O | GLY- 216 | 2.89 | 173.06 | H-Bond (Ligand Donor) |
| O0 | N | GLY- 216 | 3 | 170.53 | H-Bond (Protein Donor) |
| CD2 | CG | GLU- 217 | 4.4 | 0 | Hydrophobic |
| OH | N | GLY- 219 | 2.85 | 137.65 | H-Bond (Protein Donor) |
| CD' | SG | CYS- 220 | 4.31 | 0 | Hydrophobic |
| CF | SG | CYS- 220 | 4.43 | 0 | Hydrophobic |
| CN | SG | CYS- 220 | 3.72 | 0 | Hydrophobic |
| CL | CZ | TYR- 228 | 4.12 | 0 | Hydrophobic |
