sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.890 Å
X-ray
2008-07-11
| 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 | 94 % |
| B | 6 % |
| B-Factor: | 50.272 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.596 | 536.625 |
| % Hydrophobic | % Polar |
|---|---|
| 69.18 | 30.82 |
| According to VolSite | |
| HET Code: | R8E |
|---|---|
| Formula: | C20H13Cl2N5O2 |
| Molecular weight: | 426.256 g/mol |
| DrugBank ID: | DB08460 |
| Buried Surface Area: | 77.57 % |
| Polar Surface area: | 109.84 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 8.71524 | 11.6698 | 16.6242 |
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 |
| CL28 | CB | PRO- 95 | 3.8 | 0 | Hydrophobic |
| CL28 | CD1 | LEU- 100 | 3.85 | 0 | Hydrophobic |
| C11 | CB | LEU- 100 | 4.33 | 0 | Hydrophobic |
| C15 | CB | LEU- 100 | 4.3 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 100 | 3.83 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 100 | 3.52 | 0 | Hydrophobic |
| N20 | N | LYS- 103 | 2.83 | 160.53 | H-Bond (Protein Donor) |
| N19 | O | LYS- 103 | 3 | 120.51 | H-Bond (Ligand Donor) |
| C11 | CB | LYS- 103 | 4.02 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 106 | 4.35 | 0 | Hydrophobic |
| C8 | CB | VAL- 106 | 4.11 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 106 | 4.23 | 0 | Hydrophobic |
| C17 | CG1 | VAL- 106 | 3.46 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 179 | 3.99 | 0 | Hydrophobic |
| CL29 | CG1 | VAL- 179 | 3.26 | 0 | Hydrophobic |
| CL29 | SG | CYS- 181 | 4.13 | 0 | Hydrophobic |
| C5 | SG | CYS- 181 | 4.28 | 0 | Hydrophobic |
| CL29 | CB | TYR- 188 | 3.97 | 0 | Hydrophobic |
| C4 | CB | TYR- 188 | 3.36 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 188 | 3.92 | 0 | Aromatic Face/Face |
| CL28 | CH2 | TRP- 229 | 4.12 | 0 | Hydrophobic |
| C1 | CB | TRP- 229 | 4.17 | 0 | Hydrophobic |
| N25 | O | LEU- 234 | 3.4 | 136.64 | H-Bond (Ligand Donor) |
| C1 | CD1 | LEU- 234 | 3.7 | 0 | Hydrophobic |
| C22 | CB | LEU- 234 | 3.82 | 0 | Hydrophobic |
| C15 | CD2 | TYR- 318 | 3.61 | 0 | Hydrophobic |
