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
2010-03-31
| 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 | 91 % |
| B | 9 % |
| B-Factor: | 52.521 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.317 | 675.000 |
| % Hydrophobic | % Polar |
|---|---|
| 57.50 | 42.50 |
| According to VolSite | |
| HET Code: | 65B |
|---|---|
| Formula: | C20H15BrN6O |
| Molecular weight: | 435.277 g/mol |
| DrugBank ID: | DB06414 |
| Buried Surface Area: | 78 % |
| Polar Surface area: | 120.64 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 9.85825 | 12.6039 | 16.8192 |
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 |
| C6' | CG | PRO- 95 | 4.16 | 0 | Hydrophobic |
| C6' | CD2 | LEU- 100 | 4.23 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 100 | 4.21 | 0 | Hydrophobic |
| C21 | CG | LEU- 100 | 4.3 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 100 | 4.23 | 0 | Hydrophobic |
| N5 | O | LYS- 101 | 2.64 | 160.7 | H-Bond (Ligand Donor) |
| N16 | N | LYS- 101 | 3.35 | 128.13 | H-Bond (Protein Donor) |
| C22 | CB | ASN- 103 | 3.99 | 0 | Hydrophobic |
| C24 | CG2 | VAL- 106 | 3.59 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 106 | 3.45 | 0 | Hydrophobic |
| N18 | OE1 | GLU- 138 | 3.04 | 130.73 | H-Bond (Ligand Donor) |
| BR | CG | GLU- 138 | 3.85 | 0 | Hydrophobic |
| C2' | CG1 | VAL- 179 | 4.47 | 0 | Hydrophobic |
| BR | CG2 | VAL- 179 | 3.4 | 0 | Hydrophobic |
| C6' | CD2 | TYR- 181 | 3.74 | 0 | Hydrophobic |
| BR | CB | TYR- 181 | 3.89 | 0 | Hydrophobic |
| C1 | CB | TYR- 181 | 4.08 | 0 | Hydrophobic |
| C2' | CB | TYR- 188 | 4.01 | 0 | Hydrophobic |
| C3 | CB | TYR- 188 | 3.34 | 0 | Hydrophobic |
| C6' | CZ2 | TRP- 229 | 3.67 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 234 | 4.43 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 234 | 3.86 | 0 | Hydrophobic |
| C25 | CB | LEU- 234 | 3.94 | 0 | Hydrophobic |
