sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
1995-02-28
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1B1 |
| AC: | P03366 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11678 |
| EC Number: | 2.7.7.49 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 91 % |
| B | 9 % |
| B-Factor: | 31.708 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.740 | 381.375 |
| % Hydrophobic | % Polar |
|---|---|
| 83.19 | 16.81 |
| According to VolSite | |
| HET Code: | AAA |
|---|---|
| Formula: | C17H16Br2N2O2 |
| Molecular weight: | 440.129 g/mol |
| DrugBank ID: | DB07327 |
| Buried Surface Area: | 77.54 % |
| Polar Surface area: | 72.19 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 143.68 | -24.3841 | 75.3318 |
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 |
| C2 | CB | PRO- 95 | 4.45 | 0 | Hydrophobic |
| C1B | CD2 | LEU- 100 | 3.65 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 100 | 4.41 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 100 | 3.57 | 0 | Hydrophobic |
| BR2 | CG | LYS- 103 | 3.83 | 0 | Hydrophobic |
| C13 | CG | LYS- 103 | 3.91 | 0 | Hydrophobic |
| C8 | CG1 | VAL- 106 | 4.37 | 0 | Hydrophobic |
| BR1 | CG1 | VAL- 106 | 3.64 | 0 | Hydrophobic |
| C9 | CG2 | VAL- 106 | 3.91 | 0 | Hydrophobic |
| C1B | CG | GLU- 138 | 3.97 | 0 | Hydrophobic |
| N8B | O | VAL- 179 | 3.29 | 125.74 | H-Bond (Ligand Donor) |
| BR2 | CG1 | VAL- 179 | 3.75 | 0 | Hydrophobic |
| C1B | CD1 | TYR- 181 | 3.49 | 0 | Hydrophobic |
| C4A | CD2 | TYR- 181 | 4.41 | 0 | Hydrophobic |
| C1 | CB | TYR- 181 | 3.55 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 181 | 3.94 | 0 | Aromatic Face/Face |
| C4A | CE2 | TYR- 188 | 3.32 | 0 | Hydrophobic |
| C5 | CB | TYR- 188 | 4.16 | 0 | Hydrophobic |
| C8 | CB | TYR- 188 | 4.24 | 0 | Hydrophobic |
| BR1 | CD2 | TYR- 188 | 3.73 | 0 | Hydrophobic |
| BR1 | CD2 | PHE- 227 | 4.19 | 0 | Hydrophobic |
| C4A | CE3 | TRP- 229 | 3.31 | 0 | Hydrophobic |
| C3 | CH2 | TRP- 229 | 3.17 | 0 | Hydrophobic |
| BR1 | CD1 | LEU- 234 | 4.04 | 0 | Hydrophobic |
| C4A | CD1 | LEU- 234 | 3.78 | 0 | Hydrophobic |
| C12 | CE2 | TYR- 318 | 2.98 | 0 | Hydrophobic |
