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
2004-04-30
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.110 | 8.110 | 8.110 | 0.000 | 8.110 | 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: | 16.217 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.793 | 550.125 |
| % Hydrophobic | % Polar |
|---|---|
| 40.49 | 59.51 |
| According to VolSite | |
| HET Code: | 81A |
|---|---|
| Formula: | C20H26N3O7S2 |
| Molecular weight: | 484.566 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.93 % |
| Polar Surface area: | 176.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 17.0757 | -14.4025 | 23.4579 |
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 |
| C2A | CB | HIS- 79 | 4.19 | 0 | Hydrophobic |
| C2A | CZ | TYR- 83 | 4.42 | 0 | Hydrophobic |
| C2A | CH2 | TRP- 86 | 4.14 | 0 | Hydrophobic |
| C24 | CG | LEU- 132 | 4.32 | 0 | Hydrophobic |
| C2A | CD1 | LEU- 132 | 3.6 | 0 | Hydrophobic |
| C24 | CG2 | ILE- 209 | 4.23 | 0 | Hydrophobic |
| C26 | CD1 | ILE- 209 | 3.84 | 0 | Hydrophobic |
| N11 | OD2 | ASP- 229 | 2.61 | 159.97 | H-Bond (Ligand Donor) |
| N11 | OD1 | ASP- 229 | 3.33 | 132.42 | H-Bond (Ligand Donor) |
| CEB | CB | SER- 235 | 4.41 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 255 | 3.91 | 0 | Hydrophobic |
| C25 | CB | TRP- 257 | 4.42 | 0 | Hydrophobic |
| C4 | CB | TRP- 257 | 4.02 | 0 | Hydrophobic |
| N11 | O | GLY- 260 | 2.93 | 150.52 | H-Bond (Ligand Donor) |
