sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
1988-10-03
| Name: | Genome polyprotein |
|---|---|
| ID: | POLG_HRV14 |
| AC: | P03303 |
| Organism: | Human rhinovirus 14 |
| Reign: | Viruses |
| TaxID: | 12131 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| 1 | 95 % |
| 3 | 5 % |
| B-Factor: | 1.000 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.788 | 624.375 |
| % Hydrophobic | % Polar |
|---|---|
| 65.95 | 34.05 |
| According to VolSite | |
| HET Code: | W43 |
|---|---|
| Formula: | C21H27ClN2O3 |
| Molecular weight: | 390.904 g/mol |
| DrugBank ID: | DB08722 |
| Buried Surface Area: | 68.88 % |
| Polar Surface area: | 56.85 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 0 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| 41.3581 | 1.71452 | 124.041 |
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 |
| C4C | CD1 | ILE- 104 | 4.08 | 0 | Hydrophobic |
| C5C | CG2 | ILE- 104 | 3.97 | 0 | Hydrophobic |
| CL1 | CG2 | ILE- 104 | 4.03 | 0 | Hydrophobic |
| CL1 | CB | ASN- 105 | 4.36 | 0 | Hydrophobic |
| C6B | CD1 | LEU- 106 | 4.2 | 0 | Hydrophobic |
| C4B | CD2 | LEU- 106 | 3.68 | 0 | Hydrophobic |
| CM1 | CD1 | LEU- 116 | 4.32 | 0 | Hydrophobic |
| C5A | CG1 | VAL- 122 | 3.86 | 0 | Hydrophobic |
| C5C | CZ | TYR- 128 | 4.5 | 0 | Hydrophobic |
| C3C | CE1 | TYR- 128 | 3.65 | 0 | Hydrophobic |
| C4C | CE2 | TYR- 152 | 3.9 | 0 | Hydrophobic |
| C1C | CG | TYR- 152 | 3.9 | 0 | Hydrophobic |
| C31 | CB | PRO- 174 | 4.5 | 0 | Hydrophobic |
| C31 | CG2 | VAL- 176 | 3.3 | 0 | Hydrophobic |
| C31 | CZ | PHE- 186 | 4.4 | 0 | Hydrophobic |
| C1C | CE2 | PHE- 186 | 4.21 | 0 | Hydrophobic |
| C1C | CG2 | VAL- 188 | 4 | 0 | Hydrophobic |
| C2C | CG1 | VAL- 188 | 3.69 | 0 | Hydrophobic |
| C3C | CG2 | VAL- 188 | 3.29 | 0 | Hydrophobic |
| C4C | CG1 | VAL- 188 | 4.32 | 0 | Hydrophobic |
| C6C | CG2 | VAL- 191 | 3.28 | 0 | Hydrophobic |
| CM1 | SG | CYS- 199 | 3.8 | 0 | Hydrophobic |
| C5A | SG | CYS- 199 | 3.86 | 0 | Hydrophobic |
| N3A | ND2 | ASN- 219 | 3.39 | 121.22 | H-Bond (Protein Donor) |
| CL1 | CG | MET- 221 | 3.78 | 0 | Hydrophobic |
| C1B | SD | MET- 221 | 4.02 | 0 | Hydrophobic |
| C1C | SD | MET- 224 | 4.48 | 0 | Hydrophobic |
| N3A | O | HOH- 500 | 3.4 | 160.51 | H-Bond (Protein Donor) |
