sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.650 Å
X-ray
1997-03-17
| 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: | 51.499 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.199 | 961.875 |
| % Hydrophobic | % Polar |
|---|---|
| 51.23 | 48.77 |
| According to VolSite | |
| HET Code: | SPP |
|---|---|
| Formula: | C22H28N6O3S |
| Molecular weight: | 456.561 g/mol |
| DrugBank ID: | DB00705 |
| Buried Surface Area: | 65.23 % |
| Polar Surface area: | 118.81 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -5.60062 | -34.4731 | 23.6017 |
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 |
| C8 | CB | LEU- 100 | 4.1 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 100 | 3.64 | 0 | Hydrophobic |
| CB | CD1 | LEU- 100 | 3.61 | 0 | Hydrophobic |
| N13 | O | LYS- 103 | 3.01 | 157.95 | H-Bond (Ligand Donor) |
| O | N | LYS- 103 | 2.92 | 145.07 | H-Bond (Protein Donor) |
| C8 | CG2 | VAL- 106 | 4.49 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 106 | 3.54 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 106 | 3.89 | 0 | Hydrophobic |
| CB | CD2 | TYR- 181 | 3.97 | 0 | Hydrophobic |
| CC | CD2 | TYR- 181 | 4.01 | 0 | Hydrophobic |
| C5 | CB | TYR- 181 | 3.67 | 0 | Hydrophobic |
| CC | CD2 | TYR- 188 | 3.31 | 0 | Hydrophobic |
| C4 | CB | TYR- 188 | 3.43 | 0 | Hydrophobic |
| CE | CZ | PHE- 227 | 3.69 | 0 | Hydrophobic |
| CA | CE3 | TRP- 229 | 4.15 | 0 | Hydrophobic |
| CB | CH2 | TRP- 229 | 3.85 | 0 | Hydrophobic |
| CC | CD2 | TRP- 229 | 4.23 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 234 | 4.21 | 0 | Hydrophobic |
| CA | CD2 | LEU- 234 | 4.34 | 0 | Hydrophobic |
| C19 | CB | PRO- 236 | 3.42 | 0 | Hydrophobic |
