sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
1996-04-16
| 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: | 34.449 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.413 | 641.250 |
| % Hydrophobic | % Polar |
|---|---|
| 61.58 | 38.42 |
| According to VolSite | |
| HET Code: | TB9 |
|---|---|
| Formula: | C16H21ClN3S |
| Molecular weight: | 322.876 g/mol |
| DrugBank ID: | DB08598 |
| Buried Surface Area: | 72.13 % |
| Polar Surface area: | 51.8 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 143.819 | -24.3775 | 73.1724 |
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 |
| C15 | CG | PRO- 95 | 3.88 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 100 | 3.89 | 0 | Hydrophobic |
| C1A | CD1 | LEU- 100 | 3.58 | 0 | Hydrophobic |
| N1 | O | LYS- 101 | 3 | 142.47 | H-Bond (Ligand Donor) |
| C3A | CG2 | VAL- 106 | 4.45 | 0 | Hydrophobic |
| C7A | CG1 | VAL- 106 | 3.85 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 179 | 3.62 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 179 | 3.44 | 0 | Hydrophobic |
| C11 | CG | TYR- 181 | 4.2 | 0 | Hydrophobic |
| C16 | CE1 | TYR- 181 | 3.24 | 0 | Hydrophobic |
| C16 | CD2 | TYR- 183 | 4.34 | 0 | Hydrophobic |
| C11 | CB | TYR- 188 | 3.77 | 0 | Hydrophobic |
| C16 | CE1 | TYR- 188 | 3.75 | 0 | Hydrophobic |
| CL9 | CD2 | PHE- 227 | 4.02 | 0 | Hydrophobic |
| C15 | CZ3 | TRP- 229 | 3.24 | 0 | Hydrophobic |
| C16 | CE2 | TRP- 229 | 3.79 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 234 | 4.09 | 0 | Hydrophobic |
| CL9 | CB | LEU- 234 | 3.27 | 0 | Hydrophobic |
| CL9 | CE2 | TYR- 318 | 4.02 | 0 | Hydrophobic |
