sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2012-06-22
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.170 | 9.170 | 9.170 | 0.000 | 9.170 | 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: | 35.471 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.882 | 688.500 |
| % Hydrophobic | % Polar |
|---|---|
| 43.63 | 56.37 |
| According to VolSite | |
| HET Code: | 9MQ |
|---|---|
| Formula: | C30H36N6O6S |
| Molecular weight: | 608.708 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.4 % |
| Polar Surface area: | 198.93 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 31.684 | 13.4777 | 25.1843 |
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 |
| O23 | NE2 | HIS- 43 | 2.51 | 159.46 | H-Bond (Protein Donor) |
| C34 | CB | HIS- 43 | 3.96 | 0 | Hydrophobic |
| C34 | CB | TYR- 47 | 4.22 | 0 | Hydrophobic |
| C34 | CD2 | LEU- 96 | 4.39 | 0 | Hydrophobic |
| C28 | CD1 | LEU- 96 | 3.78 | 0 | Hydrophobic |
| C35 | CG | LEU- 96 | 3.97 | 0 | Hydrophobic |
| C26 | CD1 | ILE- 179 | 3.46 | 0 | Hydrophobic |
| C41 | OD2 | ASP- 199 | 3.47 | 0 | Ionic (Ligand Cationic) |
| C41 | OD1 | ASP- 199 | 3.58 | 0 | Ionic (Ligand Cationic) |
| N42 | OD1 | ASP- 199 | 2.89 | 156.95 | H-Bond (Ligand Donor) |
| N43 | OD2 | ASP- 199 | 2.62 | 164.78 | H-Bond (Ligand Donor) |
| C38 | CB | ALA- 200 | 4.14 | 0 | Hydrophobic |
| O23 | OG | SER- 205 | 2.61 | 170.87 | H-Bond (Protein Donor) |
| C38 | CG1 | VAL- 225 | 3.86 | 0 | Hydrophobic |
| C26 | CB | TRP- 227 | 4.28 | 0 | Hydrophobic |
| O6 | N | GLY- 228 | 3.2 | 149.94 | H-Bond (Protein Donor) |
| O15 | N | GLY- 230 | 2.96 | 141.6 | H-Bond (Protein Donor) |
| N43 | O | GLY- 230 | 2.78 | 149.76 | H-Bond (Ligand Donor) |
| C27 | SG | CYS- 231 | 4.13 | 0 | Hydrophobic |
