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
2011-10-19
| Name: | Pol protein |
|---|---|
| ID: | Q8Q3H0_9HIV1 |
| AC: | Q8Q3H0 |
| Organism: | Human immunodeficiency virus 1 |
| Reign: | Viruses |
| TaxID: | 11676 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 46 % |
| B | 54 % |
| B-Factor: | 11.077 |
|---|---|
| Number of residues: | 48 |
| Including | |
| Standard Amino Acids: | 46 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.033 | 961.875 |
| % Hydrophobic | % Polar |
|---|---|
| 40.00 | 60.00 |
| According to VolSite | |
| HET Code: | UX9 |
|---|---|
| Formula: | C42H49N5O6 |
| Molecular weight: | 719.868 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.11 % |
| Polar Surface area: | 144.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 4 |
| Rings: | 6 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 14 |
| X | Y | Z |
|---|---|---|
| 13.2554 | 21.936 | 6.55194 |
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 |
| C31 | CD2 | LEU- 23 | 4.43 | 0 | Hydrophobic |
| C16 | CB | ALA- 28 | 3.57 | 0 | Hydrophobic |
| C15 | CB | ALA- 28 | 3.66 | 0 | Hydrophobic |
| C13 | CB | ASP- 30 | 3.85 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 32 | 3.37 | 0 | Hydrophobic |
| C10 | CB | ILE- 47 | 3.93 | 0 | Hydrophobic |
| C46 | CG1 | ILE- 50 | 3.6 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 76 | 4.43 | 0 | Hydrophobic |
| C34 | CG | PRO- 81 | 3.24 | 0 | Hydrophobic |
| C28 | CB | PRO- 81 | 3.67 | 0 | Hydrophobic |
| C54 | CB | THR- 82 | 4.31 | 0 | Hydrophobic |
| C31 | CG2 | THR- 82 | 3.62 | 0 | Hydrophobic |
| C35 | CG2 | VAL- 84 | 4.16 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 84 | 3.8 | 0 | Hydrophobic |
| C27 | CD2 | LEU- 123 | 3.72 | 0 | Hydrophobic |
| O17 | OD2 | ASP- 125 | 2.6 | 174.68 | H-Bond (Ligand Donor) |
| N37 | O | GLY- 127 | 3.06 | 162.51 | H-Bond (Ligand Donor) |
| C47 | CB | ALA- 128 | 4.02 | 0 | Hydrophobic |
| O44 | N | ASP- 129 | 2.99 | 166.41 | H-Bond (Protein Donor) |
| C48 | CB | ASP- 130 | 4.42 | 0 | Hydrophobic |
| C47 | CG1 | VAL- 132 | 4.13 | 0 | Hydrophobic |
| C46 | CD1 | ILE- 147 | 3.7 | 0 | Hydrophobic |
| C48 | CD1 | ILE- 147 | 4.23 | 0 | Hydrophobic |
| N40 | O | GLY- 148 | 3.19 | 173.47 | H-Bond (Ligand Donor) |
| C16 | CG1 | ILE- 150 | 4.1 | 0 | Hydrophobic |
| C33 | CD1 | ILE- 150 | 3.72 | 0 | Hydrophobic |
| C23 | CG | PRO- 181 | 3.45 | 0 | Hydrophobic |
| C25 | CG2 | THR- 182 | 3.81 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 184 | 4.16 | 0 | Hydrophobic |
| C27 | CG1 | VAL- 184 | 4.5 | 0 | Hydrophobic |
| C47 | CG2 | VAL- 184 | 4.19 | 0 | Hydrophobic |
| O49 | O | HOH- 2051 | 3.15 | 179.96 | H-Bond (Protein Donor) |
