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
2009-06-25
| 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 | 97 % |
| B | 3 % |
| B-Factor: | 58.704 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.126 | 479.250 |
| % Hydrophobic | % Polar |
|---|---|
| 63.38 | 36.62 |
| According to VolSite | |
| HET Code: | RT7 |
|---|---|
| Formula: | C18H16Cl3N3O4S2 |
| Molecular weight: | 508.826 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 70.4 % |
| Polar Surface area: | 143.25 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 8.6056 | 10.7439 | 15.8894 |
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 |
| S12 | CD1 | LEU- 100 | 3.89 | 0 | Hydrophobic |
| C13 | CB | LEU- 100 | 4.4 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 100 | 4.04 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 100 | 3.57 | 0 | Hydrophobic |
| O23 | N | LYS- 103 | 2.74 | 167.4 | H-Bond (Protein Donor) |
| CL29 | CG2 | VAL- 106 | 3.84 | 0 | Hydrophobic |
| CL24 | CG1 | VAL- 106 | 3.95 | 0 | Hydrophobic |
| C20 | CB | VAL- 106 | 4.18 | 0 | Hydrophobic |
| N28 | O | VAL- 106 | 2.89 | 125.8 | H-Bond (Ligand Donor) |
| C10 | CG2 | VAL- 179 | 4.49 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 179 | 3.7 | 0 | Hydrophobic |
| CL30 | CD2 | TYR- 181 | 3.71 | 0 | Hydrophobic |
| C10 | CB | TYR- 181 | 3.67 | 0 | Hydrophobic |
| CL30 | CD1 | TYR- 188 | 4.33 | 0 | Hydrophobic |
| CL29 | CD2 | TYR- 188 | 4.14 | 0 | Hydrophobic |
| C2 | CB | TYR- 188 | 4.04 | 0 | Hydrophobic |
| C18 | CB | PRO- 225 | 4.36 | 0 | Hydrophobic |
| CL29 | CD2 | PHE- 227 | 4.33 | 0 | Hydrophobic |
| CL24 | CD2 | PHE- 227 | 3.69 | 0 | Hydrophobic |
| CL30 | CD2 | TRP- 229 | 3.56 | 0 | Hydrophobic |
| CL29 | CD1 | LEU- 234 | 4.34 | 0 | Hydrophobic |
| CL24 | CB | LEU- 234 | 3.95 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 234 | 3.59 | 0 | Hydrophobic |
| C18 | CG | PRO- 236 | 4.14 | 0 | Hydrophobic |
| C19 | CB | PRO- 236 | 4.26 | 0 | Hydrophobic |
| S12 | CE1 | TYR- 318 | 4.41 | 0 | Hydrophobic |
| C13 | CZ | TYR- 318 | 3.68 | 0 | Hydrophobic |
