sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2003-01-09
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 10.050 | 10.050 | 10.050 | 0.000 | 10.050 | 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 |
|---|---|
| A | 100 % |
| B-Factor: | 17.819 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.783 | 614.250 |
| % Hydrophobic | % Polar |
|---|---|
| 43.96 | 56.04 |
| According to VolSite | |
| HET Code: | L86 |
|---|---|
| Formula: | C27H35ClN6O2 |
| Molecular weight: | 511.059 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.03 % |
| Polar Surface area: | 107.01 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 16.7999 | -14.4466 | 22.3422 |
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 |
| CL2 | CB | HIS- 57 | 3.87 | 0 | Hydrophobic |
| CL2 | CE2 | TYR- 60 | 3.66 | 0 | Hydrophobic |
| CL2 | CZ3 | TRP- 60 | 3.75 | 0 | Hydrophobic |
| CL2 | CD1 | LEU- 99 | 3.9 | 0 | Hydrophobic |
| C33 | CD1 | LEU- 99 | 3.81 | 0 | Hydrophobic |
| C5 | CG | LEU- 99 | 3.73 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 174 | 4.17 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 174 | 3.91 | 0 | Hydrophobic |
| C50 | CB | ALA- 190 | 3.88 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 213 | 3.56 | 0 | Hydrophobic |
| N37 | O | SER- 214 | 2.95 | 154.89 | H-Bond (Ligand Donor) |
| C33 | CB | TRP- 215 | 4.1 | 0 | Hydrophobic |
| C8 | CB | TRP- 215 | 4.08 | 0 | Hydrophobic |
| N18 | O | GLY- 216 | 2.93 | 173.36 | H-Bond (Ligand Donor) |
| O28 | N | GLY- 216 | 3.1 | 162.97 | H-Bond (Protein Donor) |
| C11 | CG | GLU- 217 | 4.06 | 0 | Hydrophobic |
| C44 | SG | CYS- 220 | 4.25 | 0 | Hydrophobic |
| C9 | SG | CYS- 220 | 3.93 | 0 | Hydrophobic |
