sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.930 Å
X-ray
2001-09-26
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.700 | 8.850 | 8.880 | 0.090 | 8.920 | 4 |
| 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: | 23.788 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.446 | 621.000 |
| % Hydrophobic | % Polar |
|---|---|
| 35.87 | 64.13 |
| According to VolSite | |
| HET Code: | MEL |
|---|---|
| Formula: | C22H32N5O4 |
| Molecular weight: | 430.521 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.12 % |
| Polar Surface area: | 157.76 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 16.1383 | -13.0221 | 22.4072 |
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 |
| C26 | CB | HIS- 57 | 4.37 | 0 | Hydrophobic |
| C26 | CZ | TYR- 60 | 3.92 | 0 | Hydrophobic |
| C26 | CH2 | TRP- 60 | 4.02 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 99 | 4.24 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 99 | 3.68 | 0 | Hydrophobic |
| C3 | CG1 | ILE- 174 | 3.54 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 174 | 3.62 | 0 | Hydrophobic |
| C23 | OD2 | ASP- 189 | 3.62 | 0 | Ionic (Ligand Cationic) |
| C23 | OD1 | ASP- 189 | 3.61 | 0 | Ionic (Ligand Cationic) |
| N24 | OD2 | ASP- 189 | 2.9 | 136.24 | H-Bond (Ligand Donor) |
| N25 | OD1 | ASP- 189 | 2.73 | 151.57 | H-Bond (Ligand Donor) |
| C19 | CB | ALA- 190 | 4.01 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 213 | 3.87 | 0 | Hydrophobic |
| N15 | O | SER- 214 | 3.34 | 160.09 | H-Bond (Ligand Donor) |
| C1 | CE3 | TRP- 215 | 3.99 | 0 | Hydrophobic |
| C6 | CB | TRP- 215 | 4.1 | 0 | Hydrophobic |
| C5 | CE3 | TRP- 215 | 3.86 | 0 | Hydrophobic |
| N7 | O | GLY- 216 | 2.95 | 156.43 | H-Bond (Ligand Donor) |
| O0 | N | GLY- 216 | 3.15 | 162.36 | H-Bond (Protein Donor) |
| C3 | CG | GLU- 217 | 4.27 | 0 | Hydrophobic |
| N25 | O | GLY- 219 | 2.9 | 141 | H-Bond (Ligand Donor) |
| O30 | N | GLY- 219 | 2.83 | 167.5 | H-Bond (Protein Donor) |
| C21 | SG | CYS- 220 | 4.05 | 0 | Hydrophobic |
