sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.600 Å
X-ray
2008-07-18
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.000 | 7.000 | 7.000 | 0.000 | 7.000 | 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: | 19.288 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.726 | 394.875 |
| % Hydrophobic | % Polar |
|---|---|
| 46.15 | 53.85 |
| According to VolSite | |
| HET Code: | 64U |
|---|---|
| Formula: | C21H31ClN3O2 |
| Molecular weight: | 392.943 g/mol |
| DrugBank ID: | DB07190 |
| Buried Surface Area: | 64.16 % |
| Polar Surface area: | 77.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 16.5283 | -12.3844 | 22.622 |
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 |
| C17 | CZ | TYR- 60 | 4.45 | 0 | Hydrophobic |
| C3 | CE2 | TYR- 60 | 3.75 | 0 | Hydrophobic |
| C2 | CH2 | TRP- 60 | 4.24 | 0 | Hydrophobic |
| C3 | CZ2 | TRP- 60 | 3.56 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 99 | 4.48 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 99 | 4.2 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 99 | 4.21 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 99 | 4.22 | 0 | Hydrophobic |
| C12 | CG1 | ILE- 174 | 4.32 | 0 | Hydrophobic |
| CL21 | CB | ALA- 190 | 3.97 | 0 | Hydrophobic |
| C29 | CB | ALA- 190 | 3.83 | 0 | Hydrophobic |
| C30 | CG1 | VAL- 213 | 3.5 | 0 | Hydrophobic |
| N23 | O | SER- 214 | 2.91 | 170.56 | H-Bond (Ligand Donor) |
| C12 | CE3 | TRP- 215 | 3.61 | 0 | Hydrophobic |
| C13 | CD2 | TRP- 215 | 4.04 | 0 | Hydrophobic |
| C11 | CB | TRP- 215 | 4.01 | 0 | Hydrophobic |
| N | O | GLY- 216 | 2.98 | 159.26 | H-Bond (Ligand Donor) |
| O32 | N | GLY- 216 | 2.92 | 161.07 | H-Bond (Protein Donor) |
| C27 | SG | CYS- 220 | 4.24 | 0 | Hydrophobic |
| CL21 | CZ | TYR- 228 | 4.11 | 0 | Hydrophobic |
