sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.810 Å
X-ray
2001-04-27
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.220 | 4.220 | 4.220 | 0.000 | 4.220 | 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: | 24.149 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.555 | 499.500 |
| % Hydrophobic | % Polar |
|---|---|
| 44.59 | 55.41 |
| According to VolSite | |
| HET Code: | 132 |
|---|---|
| Formula: | C21H17ClN3O |
| Molecular weight: | 362.832 g/mol |
| DrugBank ID: | DB03865 |
| Buried Surface Area: | 62.97 % |
| Polar Surface area: | 87.63 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 14.4527 | -12.1802 | 19.5352 |
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 |
| C3B | SG | CYS- 42 | 3.56 | 0 | Hydrophobic |
| O6' | NE2 | HIS- 57 | 2.67 | 153.25 | H-Bond (Protein Donor) |
| DuAr | NZ | LYS- 60 | 3.78 | 59.74 | Pi/Cation |
| C5B | CD | LYS- 60 | 3.39 | 0 | Hydrophobic |
| C7 | OD2 | ASP- 189 | 3.35 | 0 | Ionic (Ligand Cationic) |
| C7 | OD1 | ASP- 189 | 3.64 | 0 | Ionic (Ligand Cationic) |
| N1 | OD2 | ASP- 189 | 2.72 | 140.29 | H-Bond (Ligand Donor) |
| N2 | OD2 | ASP- 189 | 3.21 | 124.94 | H-Bond (Ligand Donor) |
| N2 | OD1 | ASP- 189 | 2.76 | 133.24 | H-Bond (Ligand Donor) |
| CL2 | CB | ALA- 190 | 3.7 | 0 | Hydrophobic |
| C2 | CB | ALA- 190 | 3.93 | 0 | Hydrophobic |
| C4' | CG | GLU- 192 | 3.84 | 0 | Hydrophobic |
| C2' | CG | GLU- 192 | 3.66 | 0 | Hydrophobic |
| N3 | OG | SER- 195 | 2.82 | 159.18 | H-Bond (Ligand Donor) |
| C6' | CB | SER- 195 | 4.37 | 0 | Hydrophobic |
| CL2 | CG1 | VAL- 213 | 3.25 | 0 | Hydrophobic |
| N1 | O | GLY- 219 | 2.58 | 121.57 | H-Bond (Ligand Donor) |
| C6 | SG | CYS- 220 | 4.27 | 0 | Hydrophobic |
