sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.510 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 | 100 % |
| B-Factor: | 62.215 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.627 | 570.375 |
| % Hydrophobic | % Polar |
|---|---|
| 72.19 | 27.81 |
| According to VolSite | |
| HET Code: | KRV |
|---|---|
| Formula: | C18H19N3O3 |
| Molecular weight: | 325.362 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.63 % |
| 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: | 4 |
| X | Y | Z |
|---|---|---|
| 9.558 | 12.4855 | 17.5605 |
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 |
| C24 | CB | PRO- 95 | 4.33 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 100 | 4.17 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 100 | 4.08 | 0 | Hydrophobic |
| C23 | CD1 | LEU- 100 | 3.65 | 0 | Hydrophobic |
| N10 | O | LYS- 101 | 2.85 | 174.05 | H-Bond (Ligand Donor) |
| C2 | CG2 | VAL- 106 | 4.14 | 0 | Hydrophobic |
| C27 | CG1 | VAL- 106 | 4.19 | 0 | Hydrophobic |
| C26 | CG1 | VAL- 179 | 4.32 | 0 | Hydrophobic |
| C27 | CG1 | VAL- 179 | 4.2 | 0 | Hydrophobic |
| C24 | CD2 | TYR- 181 | 4.32 | 0 | Hydrophobic |
| C26 | CD1 | TYR- 181 | 3.39 | 0 | Hydrophobic |
| C24 | CD1 | TYR- 188 | 4.04 | 0 | Hydrophobic |
| C16 | CB | TYR- 188 | 4.23 | 0 | Hydrophobic |
| C25 | CB | TYR- 188 | 3.84 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 188 | 3.95 | 0 | Aromatic Face/Face |
| C2 | CE2 | PHE- 227 | 4.43 | 0 | Hydrophobic |
| C24 | CH2 | TRP- 229 | 3.81 | 0 | Hydrophobic |
| C21 | CB | TRP- 229 | 4.24 | 0 | Hydrophobic |
| C1 | CB | LEU- 234 | 4.1 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 234 | 3.65 | 0 | Hydrophobic |
| C1 | CZ | TYR- 318 | 3.91 | 0 | Hydrophobic |
