sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2010-01-06
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1H2 |
| AC: | P04585 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11706 |
| EC Number: | 2.7.7.49 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 46.750 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.698 | 529.875 |
| % Hydrophobic | % Polar |
|---|---|
| 73.89 | 26.11 |
| According to VolSite | |
| HET Code: | KR1 |
|---|---|
| Formula: | C22H20FN5O3 |
| Molecular weight: | 421.424 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.74 % |
| Polar Surface area: | 129.17 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 8.60806 | 11.2702 | 17.0217 |
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 |
| C6 | CD1 | LEU- 100 | 3.94 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 100 | 4.49 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 100 | 4.21 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 100 | 4.34 | 0 | Hydrophobic |
| N2 | O | LYS- 101 | 2.85 | 160.51 | H-Bond (Ligand Donor) |
| N4 | O | LYS- 103 | 2.75 | 140.7 | H-Bond (Ligand Donor) |
| C15 | CG1 | VAL- 106 | 4.12 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 106 | 3.73 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 179 | 3.96 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 179 | 4.18 | 0 | Hydrophobic |
| C16 | CD1 | TYR- 181 | 3.33 | 0 | Hydrophobic |
| C10 | CD1 | TYR- 188 | 3.73 | 0 | Hydrophobic |
| C14 | CB | TYR- 188 | 3.81 | 0 | Hydrophobic |
| C5 | CB | TYR- 188 | 4.21 | 0 | Hydrophobic |
| F1 | CG | PRO- 225 | 3.74 | 0 | Hydrophobic |
| F1 | CE2 | PHE- 227 | 3.7 | 0 | Hydrophobic |
| C10 | CH2 | TRP- 229 | 3.85 | 0 | Hydrophobic |
| C2 | CB | TRP- 229 | 4.22 | 0 | Hydrophobic |
| C17 | CB | LEU- 234 | 4.13 | 0 | Hydrophobic |
| C22 | CB | LEU- 234 | 4 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 234 | 3.68 | 0 | Hydrophobic |
| F1 | CG | PRO- 236 | 4.03 | 0 | Hydrophobic |
| C17 | CZ | TYR- 318 | 3.95 | 0 | Hydrophobic |
| O2 | O | HOH- 656 | 2.84 | 154.56 | H-Bond (Protein Donor) |
