sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.850 Å
X-ray
2012-09-17
| 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 | 94 % |
| B | 6 % |
| B-Factor: | 43.751 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.626 | 587.250 |
| % Hydrophobic | % Polar |
|---|---|
| 72.99 | 27.01 |
| According to VolSite | |
| HET Code: | 494 |
|---|---|
| Formula: | C21H15Cl2N3O4 |
| Molecular weight: | 444.267 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.45 % |
| Polar Surface area: | 91.66 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 271.157 | -25.0288 | 23.1046 |
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 |
| CL0 | CG | PRO- 95 | 3.4 | 0 | Hydrophobic |
| C05 | CD1 | LEU- 100 | 4.42 | 0 | Hydrophobic |
| CL0 | CD2 | LEU- 100 | 3.63 | 0 | Hydrophobic |
| C0D | CD1 | LEU- 100 | 3.85 | 0 | Hydrophobic |
| C0O | CD1 | LEU- 100 | 3.83 | 0 | Hydrophobic |
| CL7 | CG | LYS- 103 | 3.74 | 0 | Hydrophobic |
| C00 | CG | LYS- 103 | 4.01 | 0 | Hydrophobic |
| N0W | O | LYS- 103 | 3.26 | 146.34 | H-Bond (Ligand Donor) |
| O10 | N | LYS- 103 | 3.17 | 163.56 | H-Bond (Protein Donor) |
| C05 | CG2 | VAL- 106 | 3.84 | 0 | Hydrophobic |
| C04 | CG1 | VAL- 106 | 3.87 | 0 | Hydrophobic |
| C0C | CG1 | VAL- 106 | 4.3 | 0 | Hydrophobic |
| C0O | CG2 | VAL- 106 | 4.03 | 0 | Hydrophobic |
| CL7 | CG1 | VAL- 179 | 3.29 | 0 | Hydrophobic |
| CL7 | CE2 | TYR- 181 | 3.82 | 0 | Hydrophobic |
| CL0 | CD2 | TYR- 181 | 4.25 | 0 | Hydrophobic |
| C03 | CB | TYR- 188 | 4.08 | 0 | Hydrophobic |
| CL0 | CD2 | TYR- 188 | 4.36 | 0 | Hydrophobic |
| C0F | CD2 | TYR- 188 | 3.31 | 0 | Hydrophobic |
| C0C | CB | TYR- 188 | 3.71 | 0 | Hydrophobic |
| CL0 | CH2 | TRP- 229 | 3.74 | 0 | Hydrophobic |
| C0G | CD1 | LEU- 234 | 3.77 | 0 | Hydrophobic |
| C0P | CZ | TYR- 318 | 3.35 | 0 | Hydrophobic |
