sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2004-05-19
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.520 | 8.520 | 8.520 | 0.000 | 8.520 | 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 |
|---|---|
| A | 100 % |
| B-Factor: | 25.442 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 5 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.273 | 297.000 |
| % Hydrophobic | % Polar |
|---|---|
| 38.64 | 61.36 |
| According to VolSite | |
| HET Code: | 176 |
|---|---|
| Formula: | C27H28Cl2N3O2 |
| Molecular weight: | 497.436 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.03 % |
| Polar Surface area: | 77.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 16.5014 | -14.3623 | 23.5454 |
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 | 3.63 | 0 | Hydrophobic |
| CB | CH2 | TRP- 60 | 4.01 | 0 | Hydrophobic |
| CZ1 | CG | LEU- 99 | 3.81 | 0 | Hydrophobic |
| CG | CD1 | LEU- 99 | 3.86 | 0 | Hydrophobic |
| CE2 | CD1 | ILE- 174 | 4.03 | 0 | Hydrophobic |
| CE4 | CD1 | ILE- 174 | 3.95 | 0 | Hydrophobic |
| CL2 | CB | ALA- 190 | 3.7 | 0 | Hydrophobic |
| CDB | CB | ALA- 190 | 3.73 | 0 | Hydrophobic |
| CL2 | CG1 | VAL- 213 | 3.58 | 0 | Hydrophobic |
| N' | O | SER- 214 | 3.12 | 146.59 | H-Bond (Ligand Donor) |
| CB0 | CE3 | TRP- 215 | 4.36 | 0 | Hydrophobic |
| CD2 | CB | TRP- 215 | 3.8 | 0 | Hydrophobic |
| O0 | N | GLY- 216 | 2.87 | 169.58 | H-Bond (Protein Donor) |
| N0 | O | GLY- 216 | 2.63 | 165.15 | H-Bond (Ligand Donor) |
| CE4 | CG | GLU- 217 | 3.36 | 0 | Hydrophobic |
| CD' | SG | CYS- 220 | 4.26 | 0 | Hydrophobic |
| CL1 | SG | CYS- 220 | 4.03 | 0 | Hydrophobic |
| CL2 | CZ | TYR- 228 | 4.34 | 0 | Hydrophobic |
