sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.430 Å
X-ray
2005-10-21
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1B1 |
| AC: | P03366 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11678 |
| EC Number: | 2.7.7.49 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 97 % |
| B | 3 % |
| B-Factor: | 58.287 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.330 | 563.625 |
| % Hydrophobic | % Polar |
|---|---|
| 64.07 | 35.93 |
| According to VolSite | |
| HET Code: | R22 |
|---|---|
| Formula: | C20H20INO3S |
| Molecular weight: | 481.347 g/mol |
| DrugBank ID: | DB08457 |
| Buried Surface Area: | 76.52 % |
| Polar Surface area: | 76.77 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 51.0265 | -26.4357 | 27.2738 |
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 |
| C9' | CG | PRO- 95 | 3.76 | 0 | Hydrophobic |
| C9' | CD2 | LEU- 100 | 3.66 | 0 | Hydrophobic |
| C7 | CB | LEU- 100 | 3.61 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 100 | 3.96 | 0 | Hydrophobic |
| C6' | CD1 | LEU- 100 | 3.56 | 0 | Hydrophobic |
| N1 | O | LYS- 101 | 2.74 | 155.3 | H-Bond (Ligand Donor) |
| I9 | CG2 | VAL- 106 | 4.42 | 0 | Hydrophobic |
| S11 | CG1 | VAL- 106 | 3.88 | 0 | Hydrophobic |
| C2' | CG1 | VAL- 106 | 4.26 | 0 | Hydrophobic |
| I9 | CG2 | VAL- 179 | 4.25 | 0 | Hydrophobic |
| C9' | CD2 | TYR- 181 | 4.17 | 0 | Hydrophobic |
| I9 | CD1 | TYR- 181 | 3.69 | 0 | Hydrophobic |
| C8' | CE2 | TYR- 188 | 3.54 | 0 | Hydrophobic |
| I9 | CB | TYR- 188 | 4.13 | 0 | Hydrophobic |
| C4' | CD1 | TYR- 188 | 3.46 | 0 | Hydrophobic |
| C2' | CB | TYR- 188 | 3.8 | 0 | Hydrophobic |
| C8' | CB | PHE- 227 | 4.17 | 0 | Hydrophobic |
| C12 | CD2 | PHE- 227 | 3.35 | 0 | Hydrophobic |
| C8' | CB | TRP- 229 | 3.94 | 0 | Hydrophobic |
| C9' | CH2 | TRP- 229 | 4.2 | 0 | Hydrophobic |
| C12 | CB | LEU- 234 | 3.77 | 0 | Hydrophobic |
| S11 | CD1 | LEU- 234 | 3.81 | 0 | Hydrophobic |
| C3' | CD1 | LEU- 234 | 3.47 | 0 | Hydrophobic |
| C3' | CD1 | LEU- 234 | 3.47 | 0 | Hydrophobic |
| C7 | CE1 | TYR- 318 | 3.47 | 0 | Hydrophobic |
| C10 | CZ | TYR- 318 | 4.28 | 0 | Hydrophobic |
| O8 | O | HOH- 1013 | 2.84 | 172.22 | H-Bond (Protein Donor) |
