sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2008-07-25
| 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 | 97 % |
| B | 3 % |
| B-Factor: | 51.458 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.644 | 644.625 |
| % Hydrophobic | % Polar |
|---|---|
| 71.20 | 28.80 |
| According to VolSite | |
| HET Code: | PZL |
|---|---|
| Formula: | C19H10BrClFN5O |
| Molecular weight: | 458.671 g/mol |
| DrugBank ID: | DB08446 |
| Buried Surface Area: | 77.05 % |
| Polar Surface area: | 87.48 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 50.3103 | 65.5676 | 17.2764 |
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 |
| CL15 | CB | PRO- 95 | 3.89 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 100 | 4.44 | 0 | Hydrophobic |
| CL15 | CD2 | LEU- 100 | 4.13 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 100 | 4.11 | 0 | Hydrophobic |
| C7 | CB | LEU- 100 | 4.05 | 0 | Hydrophobic |
| C1 | CD2 | LEU- 100 | 4.37 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 100 | 3.89 | 0 | Hydrophobic |
| N27 | N | LYS- 103 | 2.93 | 176.69 | H-Bond (Protein Donor) |
| N28 | O | LYS- 103 | 2.78 | 157.05 | H-Bond (Ligand Donor) |
| C1 | CG | LYS- 103 | 3.55 | 0 | Hydrophobic |
| BR17 | CG1 | VAL- 106 | 4.2 | 0 | Hydrophobic |
| C25 | CG2 | VAL- 106 | 3.93 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 106 | 4.16 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 106 | 3.69 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 106 | 3.33 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 106 | 3.88 | 0 | Hydrophobic |
| C14 | CG2 | VAL- 108 | 4.21 | 0 | Hydrophobic |
| BR17 | CG1 | VAL- 179 | 4.28 | 0 | Hydrophobic |
| BR17 | CD2 | TYR- 181 | 3.72 | 0 | Hydrophobic |
| CL15 | CD1 | TYR- 188 | 4.07 | 0 | Hydrophobic |
| BR17 | CB | TYR- 188 | 3.8 | 0 | Hydrophobic |
| C9 | CB | TYR- 188 | 3.4 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 188 | 3.91 | 0 | Aromatic Face/Face |
| F5 | CD2 | PHE- 227 | 4.4 | 0 | Hydrophobic |
| C12 | CB | TRP- 229 | 4.43 | 0 | Hydrophobic |
| CL15 | CH2 | TRP- 229 | 3.85 | 0 | Hydrophobic |
| F5 | CD1 | LEU- 234 | 4.07 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 234 | 3.41 | 0 | Hydrophobic |
| C18 | CZ | TYR- 318 | 3.45 | 0 | Hydrophobic |
