sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2008-02-05
| 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 | 95 % |
| B | 5 % |
| B-Factor: | 41.633 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.385 | 594.000 |
| % Hydrophobic | % Polar |
|---|---|
| 64.20 | 35.80 |
| According to VolSite | |
| HET Code: | M14 |
|---|---|
| Formula: | C21H14Cl3N3O5S |
| Molecular weight: | 526.777 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 70.6 % |
| Polar Surface area: | 139.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 8.29221 | 10.9504 | 16.5118 |
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 |
| C8 | CD2 | LEU- 100 | 4.36 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 100 | 4.03 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 100 | 4.04 | 0 | Hydrophobic |
| C20 | CB | LEU- 100 | 4.09 | 0 | Hydrophobic |
| C10 | CB | LEU- 100 | 3.92 | 0 | Hydrophobic |
| CL1 | CG | LYS- 103 | 3.99 | 0 | Hydrophobic |
| O22 | N | LYS- 103 | 2.82 | 176.45 | H-Bond (Protein Donor) |
| CL1 | CG1 | VAL- 106 | 4.46 | 0 | Hydrophobic |
| CL2 | CG2 | VAL- 106 | 3.93 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 106 | 3.79 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 106 | 3.77 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 106 | 3.67 | 0 | Hydrophobic |
| C8 | CG1 | VAL- 106 | 3.73 | 0 | Hydrophobic |
| O24 | N | VAL- 106 | 3.04 | 167.36 | H-Bond (Protein Donor) |
| CL1 | CB | VAL- 179 | 4.27 | 0 | Hydrophobic |
| CL1 | CE2 | TYR- 181 | 3.68 | 0 | Hydrophobic |
| CL | CE2 | TYR- 188 | 3.56 | 0 | Hydrophobic |
| C7 | CB | TYR- 188 | 4.18 | 0 | Hydrophobic |
| C14 | CB | TYR- 188 | 3.33 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 188 | 3.44 | 0 | Aromatic Face/Face |
| CL | CB | PHE- 227 | 3.91 | 0 | Hydrophobic |
| CL2 | CE2 | PHE- 227 | 3.89 | 0 | Hydrophobic |
| CL | CB | TRP- 229 | 3.65 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 234 | 4.29 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 234 | 4.2 | 0 | Hydrophobic |
| C3 | CB | PRO- 236 | 3.66 | 0 | Hydrophobic |
| C20 | CE1 | TYR- 318 | 3.22 | 0 | Hydrophobic |
