sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2004-06-09
| 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: | 61.659 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.673 | 533.250 |
| % Hydrophobic | % Polar |
|---|---|
| 74.05 | 25.95 |
| According to VolSite | |
| HET Code: | H18 |
|---|---|
| Formula: | C18H22ClNO2S |
| Molecular weight: | 351.891 g/mol |
| DrugBank ID: | DB07869 |
| Buried Surface Area: | 77.32 % |
| Polar Surface area: | 65.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 1.42226 | -36.7715 | 21.7164 |
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 |
| CC | CB | PRO- 95 | 4.38 | 0 | Hydrophobic |
| CA | CD1 | LEU- 100 | 4.34 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 100 | 3.89 | 0 | Hydrophobic |
| CB | CD2 | LEU- 100 | 4.11 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 100 | 4.08 | 0 | Hydrophobic |
| N1 | O | LYS- 101 | 2.81 | 166.65 | H-Bond (Ligand Donor) |
| O2 | N | LYS- 101 | 3.27 | 154.97 | H-Bond (Protein Donor) |
| C3 | CG2 | VAL- 106 | 4.3 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 106 | 4 | 0 | Hydrophobic |
| C8 | CG2 | VAL- 106 | 4.02 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 179 | 3.42 | 0 | Hydrophobic |
| CB | CD1 | TYR- 181 | 3.7 | 0 | Hydrophobic |
| CD | CE1 | TYR- 181 | 3.66 | 0 | Hydrophobic |
| C13 | CB | TYR- 181 | 3.67 | 0 | Hydrophobic |
| CE | CE2 | TYR- 188 | 3.55 | 0 | Hydrophobic |
| C13 | CB | TYR- 188 | 4.12 | 0 | Hydrophobic |
| CF | CD2 | TYR- 188 | 3.42 | 0 | Hydrophobic |
| CL | CG | PRO- 225 | 3.69 | 0 | Hydrophobic |
| CF | CD2 | PHE- 227 | 4.47 | 0 | Hydrophobic |
| CL | CD2 | PHE- 227 | 3.41 | 0 | Hydrophobic |
| CC | CZ2 | TRP- 229 | 4.09 | 0 | Hydrophobic |
| CD | CE2 | TRP- 229 | 3.32 | 0 | Hydrophobic |
| CE | CD2 | TRP- 229 | 3.9 | 0 | Hydrophobic |
| CF | CD1 | LEU- 234 | 4.12 | 0 | Hydrophobic |
| CL | CB | LEU- 234 | 3.57 | 0 | Hydrophobic |
