sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.360 Å
X-ray
2012-10-14
| 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: | 56.342 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.926 | 499.500 |
| % Hydrophobic | % Polar |
|---|---|
| 77.03 | 22.97 |
| According to VolSite | |
| HET Code: | WHU |
|---|---|
| Formula: | C18H11BrCl2FN5O2 |
| Molecular weight: | 499.121 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.39 % |
| Polar Surface area: | 116.82 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -8.40541 | 65.9694 | 16.9794 |
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 |
| CL2 | CB | PRO- 95 | 4.17 | 0 | Hydrophobic |
| C13 | CB | LEU- 100 | 4 | 0 | Hydrophobic |
| CL2 | CD1 | LEU- 100 | 3.89 | 0 | Hydrophobic |
| C20 | CD1 | LEU- 100 | 3.73 | 0 | Hydrophobic |
| F29 | CD1 | LEU- 100 | 3.64 | 0 | Hydrophobic |
| O09 | N | LYS- 103 | 2.65 | 166.48 | H-Bond (Protein Donor) |
| C14 | CG | LYS- 103 | 4.01 | 0 | Hydrophobic |
| N01 | O | LYS- 104 | 2.6 | 149.35 | H-Bond (Ligand Donor) |
| C17 | CG1 | VAL- 106 | 3.75 | 0 | Hydrophobic |
| F29 | CG1 | VAL- 106 | 4.27 | 0 | Hydrophobic |
| C27 | CG1 | VAL- 106 | 4.24 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 106 | 3.83 | 0 | Hydrophobic |
| C27 | CG2 | VAL- 108 | 4.1 | 0 | Hydrophobic |
| BR | CG2 | VAL- 179 | 3.66 | 0 | Hydrophobic |
| C14 | CG2 | VAL- 179 | 4.38 | 0 | Hydrophobic |
| BR | CD2 | TYR- 181 | 3.68 | 0 | Hydrophobic |
| BR | CB | LEU- 188 | 3.95 | 0 | Hydrophobic |
| C19 | CB | LEU- 188 | 3.65 | 0 | Hydrophobic |
| CL2 | CD1 | LEU- 188 | 3.91 | 0 | Hydrophobic |
| C21 | CD1 | LEU- 188 | 3.33 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 188 | 3.38 | 0 | Hydrophobic |
| CL | CD2 | PHE- 227 | 3.88 | 0 | Hydrophobic |
| CL2 | CH2 | TRP- 229 | 3.63 | 0 | Hydrophobic |
| CL | CB | LEU- 234 | 4.47 | 0 | Hydrophobic |
| F29 | CD1 | LEU- 234 | 3.83 | 0 | Hydrophobic |
| C21 | CD1 | LEU- 234 | 3.66 | 0 | Hydrophobic |
| C23 | CD1 | LEU- 234 | 3.26 | 0 | Hydrophobic |
