sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2008-12-03
| 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: | 80.842 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.414 | 1346.625 |
| % Hydrophobic | % Polar |
|---|---|
| 54.64 | 45.36 |
| According to VolSite | |
| HET Code: | 3OB |
|---|---|
| Formula: | C25H23ClN4O3 |
| Molecular weight: | 462.928 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 76.53 % |
| Polar Surface area: | 85.67 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 49.7352 | 64.9358 | 16.2488 |
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 |
| CL9 | CB | PRO- 95 | 3.97 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 100 | 4.11 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 100 | 3.69 | 0 | Hydrophobic |
| CL9 | CD2 | LEU- 100 | 3.93 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 100 | 4.12 | 0 | Hydrophobic |
| C20 | CB | LEU- 100 | 3.98 | 0 | Hydrophobic |
| N13 | O | LYS- 101 | 2.78 | 170.09 | H-Bond (Ligand Donor) |
| O23 | N | LYS- 103 | 2.8 | 150.73 | H-Bond (Protein Donor) |
| C6 | CG1 | VAL- 106 | 4.47 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 106 | 4.48 | 0 | Hydrophobic |
| C29 | CG2 | VAL- 106 | 4.04 | 0 | Hydrophobic |
| C28 | CB | VAL- 106 | 3.74 | 0 | Hydrophobic |
| C33 | CB | VAL- 106 | 3.91 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 179 | 3.65 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 179 | 3.55 | 0 | Hydrophobic |
| CL9 | CD2 | TYR- 181 | 3.56 | 0 | Hydrophobic |
| C18 | CB | TYR- 181 | 3.61 | 0 | Hydrophobic |
| C5 | CB | TYR- 188 | 3.6 | 0 | Hydrophobic |
| C6 | CG | TYR- 188 | 3.46 | 0 | Hydrophobic |
| C32 | CG | PRO- 225 | 3.84 | 0 | Hydrophobic |
| C33 | CB | PRO- 225 | 3.86 | 0 | Hydrophobic |
| C26 | CE2 | PHE- 227 | 3.86 | 0 | Hydrophobic |
| CL9 | CH2 | TRP- 229 | 3.39 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 234 | 3.37 | 0 | Hydrophobic |
| C30 | CB | PRO- 236 | 4.37 | 0 | Hydrophobic |
| C20 | CE2 | TYR- 318 | 3.55 | 0 | Hydrophobic |
