sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.650 Å
X-ray
2008-06-19
| 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: | 48.083 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.645 | 415.125 |
| % Hydrophobic | % Polar |
|---|---|
| 73.98 | 26.02 |
| According to VolSite | |
| HET Code: | PDZ |
|---|---|
| Formula: | C17H12ClFN2O2 |
| Molecular weight: | 330.741 g/mol |
| DrugBank ID: | DB08379 |
| Buried Surface Area: | 76.75 % |
| Polar Surface area: | 50.69 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 49.8977 | 64.2652 | 16.6296 |
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 |
| C3 | CG | PRO- 95 | 4.27 | 0 | Hydrophobic |
| C11 | CB | LEU- 100 | 4.44 | 0 | Hydrophobic |
| C14 | CB | LEU- 100 | 4.01 | 0 | Hydrophobic |
| F16 | CD1 | LEU- 100 | 3.53 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 100 | 3.64 | 0 | Hydrophobic |
| N21 | O | LYS- 103 | 2.65 | 165.65 | H-Bond (Ligand Donor) |
| N22 | N | LYS- 103 | 3.09 | 167.72 | H-Bond (Protein Donor) |
| C10 | CG | LYS- 103 | 3.78 | 0 | Hydrophobic |
| C8 | CG1 | VAL- 106 | 3.96 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 106 | 3.97 | 0 | Hydrophobic |
| CL15 | CG1 | VAL- 179 | 4.08 | 0 | Hydrophobic |
| CL15 | CB | TYR- 181 | 4.49 | 0 | Hydrophobic |
| C4 | CB | TYR- 181 | 4.08 | 0 | Hydrophobic |
| CL15 | CB | TYR- 188 | 3.8 | 0 | Hydrophobic |
| C6 | CD2 | TYR- 188 | 3.4 | 0 | Hydrophobic |
| C5 | CB | TYR- 188 | 3.7 | 0 | Hydrophobic |
| C1 | CB | TRP- 229 | 4.41 | 0 | Hydrophobic |
| F16 | CD1 | LEU- 234 | 3.73 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 234 | 3.54 | 0 | Hydrophobic |
| C14 | CE2 | TYR- 318 | 3.5 | 0 | Hydrophobic |
