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: | 7.680 | 7.680 | 7.680 | 0.000 | 7.680 | 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: | 24.083 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.706 | 540.000 |
| % Hydrophobic | % Polar |
|---|---|
| 45.63 | 54.38 |
| According to VolSite | |
| HET Code: | 14A |
|---|---|
| Formula: | C19H28ClN4O3 |
| Molecular weight: | 395.904 g/mol |
| DrugBank ID: | DB06859 |
| Buried Surface Area: | 61.76 % |
| Polar Surface area: | 102.41 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 16.8037 | -14.1218 | 23.3931 |
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 |
| CL16 | CB | HIS- 79 | 4.16 | 0 | Hydrophobic |
| CL16 | CE2 | TYR- 83 | 3.74 | 0 | Hydrophobic |
| CL16 | CZ3 | TRP- 86 | 3.86 | 0 | Hydrophobic |
| C25 | CG | LEU- 132 | 4.13 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 132 | 3.91 | 0 | Hydrophobic |
| C26 | CD1 | ILE- 209 | 3.67 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 229 | 2.54 | 162.25 | H-Bond (Ligand Donor) |
| N1 | OD1 | ASP- 229 | 3.4 | 130.36 | H-Bond (Ligand Donor) |
| N3 | OD1 | ASP- 229 | 2.88 | 152.16 | H-Bond (Ligand Donor) |
| C6 | CG1 | VAL- 255 | 3.96 | 0 | Hydrophobic |
| C26 | CD2 | TRP- 257 | 4.09 | 0 | Hydrophobic |
| C27 | CE3 | TRP- 257 | 3.56 | 0 | Hydrophobic |
| C10 | CB | TRP- 257 | 3.9 | 0 | Hydrophobic |
| N1 | O | GLY- 260 | 2.85 | 159.47 | H-Bond (Ligand Donor) |
