sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
1999-07-21
| 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: | 41.532 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.535 | 934.875 |
| % Hydrophobic | % Polar |
|---|---|
| 62.45 | 37.55 |
| According to VolSite | |
| HET Code: | GCA |
|---|---|
| Formula: | C19H26N2O3 |
| Molecular weight: | 330.421 g/mol |
| DrugBank ID: | DB07820 |
| Buried Surface Area: | 76.7 % |
| Polar Surface area: | 58.64 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -1.67204 | -34.4929 | 25.7788 |
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 |
| CP | CB | PRO- 95 | 4.07 | 0 | Hydrophobic |
| CP | CD2 | LEU- 100 | 4.01 | 0 | Hydrophobic |
| CI | CD2 | LEU- 100 | 4.48 | 0 | Hydrophobic |
| CA | CD1 | LEU- 100 | 3.95 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 100 | 3.66 | 0 | Hydrophobic |
| N10 | O | LYS- 101 | 2.94 | 169.44 | H-Bond (Ligand Donor) |
| CG | CG1 | VAL- 106 | 3.95 | 0 | Hydrophobic |
| CH | CG1 | VAL- 106 | 4.18 | 0 | Hydrophobic |
| CD | CG2 | VAL- 106 | 4.22 | 0 | Hydrophobic |
| CF | CG1 | VAL- 179 | 4.12 | 0 | Hydrophobic |
| CP | CE1 | TYR- 181 | 4 | 0 | Hydrophobic |
| CI | CB | TYR- 181 | 3.36 | 0 | Hydrophobic |
| CQ | CE2 | TYR- 188 | 3.59 | 0 | Hydrophobic |
| CH | CB | TYR- 188 | 3.79 | 0 | Hydrophobic |
| C6 | CD2 | TYR- 188 | 3.49 | 0 | Hydrophobic |
| CG | CB | TYR- 188 | 4.17 | 0 | Hydrophobic |
| CD | CG | PRO- 225 | 4.11 | 0 | Hydrophobic |
| CQ | CB | PHE- 227 | 3.83 | 0 | Hydrophobic |
| CC | CD2 | PHE- 227 | 4.23 | 0 | Hydrophobic |
| CD | CE2 | PHE- 227 | 3.83 | 0 | Hydrophobic |
| CP | CH2 | TRP- 229 | 3.67 | 0 | Hydrophobic |
| CQ | CB | TRP- 229 | 3.79 | 0 | Hydrophobic |
| C6 | CG | LEU- 234 | 4.45 | 0 | Hydrophobic |
| CA | CB | LEU- 234 | 3.93 | 0 | Hydrophobic |
| CC | CB | LEU- 234 | 4.08 | 0 | Hydrophobic |
| CQ | CD2 | LEU- 234 | 4.18 | 0 | Hydrophobic |
| CD | CB | PRO- 236 | 4.09 | 0 | Hydrophobic |
| O9 | O | HOH- 1043 | 2.88 | 138.19 | H-Bond (Protein Donor) |
