sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2012-06-22
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.170 | 8.170 | 8.170 | 0.000 | 8.170 | 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: | 42.004 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.689 | 634.500 |
| % Hydrophobic | % Polar |
|---|---|
| 42.02 | 57.98 |
| According to VolSite | |
| HET Code: | 9MX |
|---|---|
| Formula: | C28H38N6O6S |
| Molecular weight: | 586.703 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.23 % |
| Polar Surface area: | 198.93 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| 31.4466 | 13.6963 | 25.196 |
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 |
| C29 | CB | HIS- 43 | 4.3 | 0 | Hydrophobic |
| C29 | CE1 | TYR- 47 | 3.38 | 0 | Hydrophobic |
| C28 | CH2 | TRP- 50 | 3.51 | 0 | Hydrophobic |
| C30 | CD1 | LEU- 96 | 4.47 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 96 | 3.46 | 0 | Hydrophobic |
| C29 | CD1 | LEU- 96 | 4.45 | 0 | Hydrophobic |
| C39 | CG | LEU- 96 | 3.74 | 0 | Hydrophobic |
| C26 | CD1 | ILE- 179 | 3.71 | 0 | Hydrophobic |
| C41 | OD2 | ASP- 199 | 3.66 | 0 | Ionic (Ligand Cationic) |
| C41 | OD1 | ASP- 199 | 3.66 | 0 | Ionic (Ligand Cationic) |
| N43 | OD2 | ASP- 199 | 2.8 | 141.04 | H-Bond (Ligand Donor) |
| N42 | OD1 | ASP- 199 | 3.02 | 136.58 | H-Bond (Ligand Donor) |
| C40 | CB | ALA- 200 | 3.99 | 0 | Hydrophobic |
| C40 | CG1 | VAL- 225 | 3.68 | 0 | Hydrophobic |
| C26 | CB | TRP- 227 | 4.29 | 0 | Hydrophobic |
| N3 | O | GLY- 228 | 2.71 | 127.01 | H-Bond (Ligand Donor) |
| O6 | N | GLY- 228 | 3.05 | 163.85 | H-Bond (Protein Donor) |
| N43 | O | GLY- 230 | 2.91 | 140.96 | H-Bond (Ligand Donor) |
| O15 | N | GLY- 230 | 3.09 | 132.9 | H-Bond (Protein Donor) |
| C27 | SG | CYS- 231 | 4.16 | 0 | Hydrophobic |
