sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.950 Å
X-ray
2010-06-03
| 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 | 94 % |
| B | 6 % |
| B-Factor: | 80.059 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.789 | 982.125 |
| % Hydrophobic | % Polar |
|---|---|
| 63.23 | 36.77 |
| According to VolSite | |
| HET Code: | JGZ |
|---|---|
| Formula: | C24H26N6O3S |
| Molecular weight: | 478.567 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.22 % |
| Polar Surface area: | 142.6 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 51.1098 | 65.5017 | 16.5644 |
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 |
| C27 | CB | PRO- 95 | 4.02 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 100 | 3.83 | 0 | Hydrophobic |
| C26 | CD1 | LEU- 100 | 4.41 | 0 | Hydrophobic |
| C27 | CD2 | LEU- 100 | 3.91 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 100 | 3.74 | 0 | Hydrophobic |
| N4 | N | LYS- 101 | 3.31 | 158.46 | H-Bond (Protein Donor) |
| N9 | O | LYS- 101 | 2.78 | 157.17 | H-Bond (Ligand Donor) |
| C15 | CB | LYS- 103 | 4.05 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 106 | 4.09 | 0 | Hydrophobic |
| C28 | CG1 | VAL- 106 | 4.26 | 0 | Hydrophobic |
| C14 | CG1 | VAL- 106 | 3.42 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 106 | 3.33 | 0 | Hydrophobic |
| C2 | CG | GLU- 138 | 3.94 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 179 | 3.52 | 0 | Hydrophobic |
| C28 | CG1 | VAL- 179 | 3.59 | 0 | Hydrophobic |
| C27 | CD2 | TYR- 181 | 3.52 | 0 | Hydrophobic |
| C8 | CB | TYR- 181 | 3.74 | 0 | Hydrophobic |
| C28 | CB | TYR- 188 | 4.18 | 0 | Hydrophobic |
| C23 | CB | TYR- 188 | 3.53 | 0 | Hydrophobic |
| C20 | CB | PHE- 227 | 4.47 | 0 | Hydrophobic |
| C27 | CZ2 | TRP- 229 | 3.57 | 0 | Hydrophobic |
| C21 | CB | LEU- 234 | 4.22 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 234 | 4.11 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 234 | 3.98 | 0 | Hydrophobic |
| C18 | CB | PRO- 236 | 3.94 | 0 | Hydrophobic |
| C12 | CZ | TYR- 318 | 3.45 | 0 | Hydrophobic |
