sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2000-03-27
| 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 | 97 % |
| B | 3 % |
| B-Factor: | 60.499 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.496 | 806.625 |
| % Hydrophobic | % Polar |
|---|---|
| 57.74 | 42.26 |
| According to VolSite | |
| HET Code: | S11 |
|---|---|
| Formula: | C20H20Cl2N4O2S |
| Molecular weight: | 451.369 g/mol |
| DrugBank ID: | DB08502 |
| Buried Surface Area: | 74.89 % |
| Polar Surface area: | 108.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 0.186483 | -41.6993 | 26.1685 |
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 |
| C14 | CD2 | LEU- 100 | 4.04 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 100 | 4.3 | 0 | Hydrophobic |
| CA | CB | LEU- 100 | 3.78 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 100 | 3.78 | 0 | Hydrophobic |
| O25 | N | LYS- 103 | 2.7 | 176.14 | H-Bond (Protein Donor) |
| S1 | CG1 | VAL- 106 | 4.17 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 106 | 3.64 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 106 | 3.58 | 0 | Hydrophobic |
| C13 | CB | VAL- 179 | 4.16 | 0 | Hydrophobic |
| C14 | CG1 | VAL- 179 | 4.16 | 0 | Hydrophobic |
| CL2 | CE1 | TYR- 181 | 3.78 | 0 | Hydrophobic |
| C14 | CB | TYR- 181 | 3.78 | 0 | Hydrophobic |
| CL1 | CD1 | TYR- 183 | 4.39 | 0 | Hydrophobic |
| S1 | CD2 | TYR- 188 | 3.48 | 0 | Hydrophobic |
| CL1 | CZ | TYR- 188 | 3.8 | 0 | Hydrophobic |
| C6 | CB | TYR- 188 | 4.24 | 0 | Hydrophobic |
| C12 | CB | TYR- 188 | 3.88 | 0 | Hydrophobic |
| S1 | CD2 | PHE- 227 | 3.91 | 0 | Hydrophobic |
| CL1 | CB | PHE- 227 | 4.17 | 0 | Hydrophobic |
| C21 | CD2 | PHE- 227 | 3.39 | 0 | Hydrophobic |
| C7 | CB | PHE- 227 | 4.2 | 0 | Hydrophobic |
| CL2 | CZ2 | TRP- 229 | 3.81 | 0 | Hydrophobic |
| CL1 | CB | TRP- 229 | 3.81 | 0 | Hydrophobic |
| C15 | CB | LEU- 234 | 4.37 | 0 | Hydrophobic |
| C21 | CB | LEU- 234 | 3.94 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 234 | 3.8 | 0 | Hydrophobic |
| N24 | O | PRO- 236 | 3.03 | 139.97 | H-Bond (Ligand Donor) |
| C15 | CZ | TYR- 318 | 4 | 0 | Hydrophobic |
| CA | CD1 | TYR- 318 | 3.84 | 0 | Hydrophobic |
