sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.850 Å
X-ray
2010-08-04
| Name: | Pol polyprotein |
|---|---|
| ID: | Q90K99_9HIV1 |
| AC: | Q90K99 |
| Organism: | Human immunodeficiency virus 1 |
| Reign: | Viruses |
| TaxID: | 11676 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 48 % |
| B | 52 % |
| B-Factor: | 22.552 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.861 | 678.375 |
| % Hydrophobic | % Polar |
|---|---|
| 42.29 | 57.71 |
| According to VolSite | |
| HET Code: | K19 |
|---|---|
| Formula: | C29H37N3O7S2 |
| Molecular weight: | 603.750 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.05 % |
| Polar Surface area: | 163.91 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 19.507 | 30.0379 | 14.1565 |
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 |
| C15 | CD2 | LEU- 23 | 4.1 | 0 | Hydrophobic |
| C37 | CD1 | LEU- 23 | 3.88 | 0 | Hydrophobic |
| O18 | OD1 | ASP- 25 | 2.57 | 164.72 | H-Bond (Ligand Donor) |
| O18 | OD1 | ASP- 25 | 2.56 | 166.29 | H-Bond (Protein Donor) |
| N20 | O | GLY- 27 | 3.18 | 152.02 | H-Bond (Ligand Donor) |
| C16 | CB | ALA- 28 | 4.46 | 0 | Hydrophobic |
| C7 | CB | ALA- 28 | 3.36 | 0 | Hydrophobic |
| C25 | CB | ALA- 28 | 3.74 | 0 | Hydrophobic |
| C27 | CB | ASP- 29 | 3.87 | 0 | Hydrophobic |
| C29 | CB | ASP- 29 | 4.38 | 0 | Hydrophobic |
| O28 | N | ASP- 29 | 2.96 | 156.55 | H-Bond (Protein Donor) |
| N1 | N | ASP- 30 | 3.18 | 144.56 | H-Bond (Protein Donor) |
| O26 | N | ASP- 30 | 3.07 | 162.59 | H-Bond (Protein Donor) |
| C25 | CB | ASP- 30 | 4.31 | 0 | Hydrophobic |
| C25 | CG2 | VAL- 32 | 4.02 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 32 | 3.72 | 0 | Hydrophobic |
| S1 | CB | ILE- 47 | 3.8 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 50 | 4.36 | 0 | Hydrophobic |
| C24 | CD1 | ILE- 50 | 3.86 | 0 | Hydrophobic |
| C33 | CB | ILE- 50 | 4.23 | 0 | Hydrophobic |
| C18 | CG | PRO- 81 | 3.68 | 0 | Hydrophobic |
| C34 | CG | PRO- 81 | 3.73 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 82 | 3.85 | 0 | Hydrophobic |
| C36 | CG2 | VAL- 82 | 3.58 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 84 | 4.31 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 84 | 4.28 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 84 | 4.19 | 0 | Hydrophobic |
| C25 | CD1 | ILE- 84 | 4.1 | 0 | Hydrophobic |
| C32 | CD1 | ILE- 84 | 3.94 | 0 | Hydrophobic |
