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
2007-10-16
| Name: | Pol protein |
|---|---|
| ID: | A0F7J4_9HIV1 |
| AC: | A0F7J4 |
| Organism: | Human immunodeficiency virus 1 |
| Reign: | Viruses |
| TaxID: | 11676 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 49 % |
| B | 51 % |
| B-Factor: | 29.724 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 43 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.141 | 914.625 |
| % Hydrophobic | % Polar |
|---|---|
| 44.65 | 55.35 |
| According to VolSite | |
| HET Code: | AB1 |
|---|---|
| Formula: | C37H48N4O5 |
| Molecular weight: | 628.801 g/mol |
| DrugBank ID: | DB01601 |
| Buried Surface Area: | 62.84 % |
| Polar Surface area: | 120 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 15 |
| X | Y | Z |
|---|---|---|
| -18.1231 | 0.583283 | -0.707174 |
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 |
| C22 | CD2 | LEU- 23 | 4.44 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 23 | 3.64 | 0 | Hydrophobic |
| O4 | OD1 | ASP- 25 | 2.92 | 151.47 | H-Bond (Ligand Donor) |
| O4 | OD2 | ASP- 25 | 2.9 | 136.93 | H-Bond (Ligand Donor) |
| O4 | OD2 | ASP- 25 | 2.63 | 146.82 | H-Bond (Protein Donor) |
| N3 | O | GLY- 27 | 3.09 | 164.93 | H-Bond (Ligand Donor) |
| C36 | CB | ALA- 28 | 3.93 | 0 | Hydrophobic |
| C14 | CB | ALA- 28 | 3.74 | 0 | Hydrophobic |
| O1 | N | ASP- 29 | 2.77 | 155.67 | H-Bond (Protein Donor) |
| C32 | CB | ASP- 29 | 3.67 | 0 | Hydrophobic |
| C15 | CB | ASP- 30 | 4.17 | 0 | Hydrophobic |
| C30 | CB | ASP- 30 | 4.29 | 0 | Hydrophobic |
| C31 | CB | ASP- 30 | 3.46 | 0 | Hydrophobic |
| C36 | CD1 | ILE- 32 | 3.29 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 32 | 3.8 | 0 | Hydrophobic |
| C31 | CG1 | VAL- 47 | 4.28 | 0 | Hydrophobic |
| C27 | CD1 | ILE- 50 | 4.25 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 50 | 3.73 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 50 | 3.52 | 0 | Hydrophobic |
| C7 | CB | PRO- 81 | 4.46 | 0 | Hydrophobic |
| C8 | CG | PRO- 81 | 4.37 | 0 | Hydrophobic |
| C17 | CB | PRO- 81 | 4.18 | 0 | Hydrophobic |
| C16 | CG | PRO- 81 | 3.45 | 0 | Hydrophobic |
| C6 | CB | ALA- 82 | 3.57 | 0 | Hydrophobic |
| C19 | CB | ALA- 82 | 4.19 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 84 | 3.77 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 84 | 3.87 | 0 | Hydrophobic |
| C23 | CD1 | ILE- 84 | 4.38 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 84 | 3.65 | 0 | Hydrophobic |
