sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 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 | 96 % |
| B | 4 % |
| B-Factor: | 55.577 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.327 | 573.750 |
| % Hydrophobic | % Polar |
|---|---|
| 68.82 | 31.18 |
| According to VolSite | |
| HET Code: | H12 |
|---|---|
| Formula: | C18H22ClNO2 |
| Molecular weight: | 319.826 g/mol |
| DrugBank ID: | DB07867 |
| Buried Surface Area: | 75.3 % |
| Polar Surface area: | 38.33 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 |
|---|---|---|
| 1.44591 | -36.856 | 20.983 |
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 |
| CA | CD1 | LEU- 100 | 4.19 | 0 | Hydrophobic |
| CB | CD2 | LEU- 100 | 4.16 | 0 | Hydrophobic |
| C2 | CB | LEU- 100 | 3.97 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 100 | 4.17 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 100 | 3.95 | 0 | Hydrophobic |
| N1 | O | LYS- 101 | 2.55 | 163.22 | H-Bond (Ligand Donor) |
| O2 | N | LYS- 101 | 3.32 | 170.09 | H-Bond (Protein Donor) |
| C2 | CG | LYS- 103 | 3.9 | 0 | Hydrophobic |
| CL | CB | VAL- 106 | 4.41 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 106 | 3.78 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 179 | 3.45 | 0 | Hydrophobic |
| CB | CD1 | TYR- 181 | 3.72 | 0 | Hydrophobic |
| C13 | CB | TYR- 181 | 3.71 | 0 | Hydrophobic |
| CD | CZ | TYR- 188 | 4.19 | 0 | Hydrophobic |
| CE | CE2 | TYR- 188 | 3.56 | 0 | Hydrophobic |
| CF | CD2 | TYR- 188 | 3.3 | 0 | Hydrophobic |
| C13 | CB | TYR- 188 | 4.02 | 0 | Hydrophobic |
| CL | CG | PRO- 225 | 4.31 | 0 | Hydrophobic |
| CF | CD2 | PHE- 227 | 4.35 | 0 | Hydrophobic |
| CL | CD2 | PHE- 227 | 3.75 | 0 | Hydrophobic |
| CC | CZ2 | TRP- 229 | 4.02 | 0 | Hydrophobic |
| CD | CE2 | TRP- 229 | 3.76 | 0 | Hydrophobic |
| CE | CD2 | TRP- 229 | 4.48 | 0 | Hydrophobic |
| CE | CD1 | LEU- 234 | 4 | 0 | Hydrophobic |
| CL | CB | LEU- 234 | 3.82 | 0 | Hydrophobic |
