sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.550 Å
X-ray
2010-01-06
| 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: | 69.080 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.968 | 540.000 |
| % Hydrophobic | % Polar |
|---|---|
| 76.88 | 23.13 |
| According to VolSite | |
| HET Code: | KBT |
|---|---|
| Formula: | C20H23N3O3 |
| Molecular weight: | 353.415 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 76.1 % |
| Polar Surface area: | 90.27 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| 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 |
|---|---|---|
| 9.52723 | 12.4059 | 17.4328 |
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 |
| C16 | CG | PRO- 95 | 4 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 100 | 4.19 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 100 | 4.23 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 100 | 3.63 | 0 | Hydrophobic |
| N24 | O | LYS- 101 | 2.98 | 166.62 | H-Bond (Ligand Donor) |
| C1 | CG1 | VAL- 106 | 4.08 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 106 | 3.86 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 179 | 3.98 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 179 | 4.25 | 0 | Hydrophobic |
| C16 | CD2 | TYR- 181 | 3.72 | 0 | Hydrophobic |
| C20 | CB | TYR- 181 | 3.61 | 0 | Hydrophobic |
| C10 | CB | TYR- 188 | 4.2 | 0 | Hydrophobic |
| C19 | CB | TYR- 188 | 3.89 | 0 | Hydrophobic |
| C3 | CB | PRO- 225 | 3.95 | 0 | Hydrophobic |
| C2 | CD2 | PHE- 227 | 3.61 | 0 | Hydrophobic |
| C3 | CE2 | PHE- 227 | 3.7 | 0 | Hydrophobic |
| C16 | CH2 | TRP- 229 | 3.7 | 0 | Hydrophobic |
| C11 | CB | TRP- 229 | 4.32 | 0 | Hydrophobic |
| C2 | CB | LEU- 234 | 3.81 | 0 | Hydrophobic |
| C4 | CB | LEU- 234 | 4.19 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 234 | 3.47 | 0 | Hydrophobic |
| C3 | CG | PRO- 236 | 4.41 | 0 | Hydrophobic |
| C4 | CZ | TYR- 318 | 4.1 | 0 | Hydrophobic |
| O26 | O | HOH- 586 | 2.61 | 120.44 | H-Bond (Protein Donor) |
