sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2007-10-16
| 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 | 97 % |
| B | 3 % |
| B-Factor: | 46.384 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.598 | 378.000 |
| % Hydrophobic | % Polar |
|---|---|
| 75.89 | 24.11 |
| According to VolSite | |
| HET Code: | TT1 |
|---|---|
| Formula: | C20H16ClN3S2 |
| Molecular weight: | 397.944 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 80.38 % |
| Polar Surface area: | 84.25 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 9.27365 | 12.6111 | 16.5597 |
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 |
| C6 | CB | PRO- 95 | 4.04 | 0 | Hydrophobic |
| S9 | CD1 | LEU- 100 | 4.17 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 100 | 4.39 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 100 | 3.6 | 0 | Hydrophobic |
| CL22 | CG | LYS- 103 | 3.3 | 0 | Hydrophobic |
| N18 | NZ | LYS- 103 | 2.89 | 159.44 | H-Bond (Protein Donor) |
| CL22 | CG2 | VAL- 106 | 3.82 | 0 | Hydrophobic |
| S14 | CG2 | VAL- 106 | 4.17 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 106 | 3.76 | 0 | Hydrophobic |
| C24 | CB | VAL- 106 | 4.12 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 106 | 3.63 | 0 | Hydrophobic |
| S14 | CG2 | VAL- 179 | 4.37 | 0 | Hydrophobic |
| C7 | CB | TYR- 181 | 4.44 | 0 | Hydrophobic |
| S14 | CB | TYR- 188 | 3.99 | 0 | Hydrophobic |
| C1 | CB | TYR- 188 | 3.82 | 0 | Hydrophobic |
| C25 | CG | PRO- 225 | 3.45 | 0 | Hydrophobic |
| S9 | CD2 | PHE- 227 | 4.18 | 0 | Hydrophobic |
| C4 | CB | TRP- 229 | 4.26 | 0 | Hydrophobic |
| S9 | CB | LEU- 234 | 3.73 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 234 | 3.66 | 0 | Hydrophobic |
| C23 | CB | PRO- 236 | 3.6 | 0 | Hydrophobic |
| C8 | CZ | TYR- 318 | 3.4 | 0 | Hydrophobic |
