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 | 97 % |
| B | 3 % |
| B-Factor: | 46.782 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.452 | 600.750 |
| % Hydrophobic | % Polar |
|---|---|
| 69.10 | 30.90 |
| According to VolSite | |
| HET Code: | M22 |
|---|---|
| Formula: | C21H13Cl2N3O2 |
| Molecular weight: | 410.253 g/mol |
| DrugBank ID: | DB08154 |
| Buried Surface Area: | 79.21 % |
| Polar Surface area: | 70.93 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 8.55739 | 11.542 | 16.8425 |
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 |
| CL | CB | PRO- 95 | 3.85 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 100 | 3.61 | 0 | Hydrophobic |
| CL | CD1 | LEU- 100 | 4.1 | 0 | Hydrophobic |
| C13 | CB | LEU- 100 | 4.26 | 0 | Hydrophobic |
| C4 | CB | LEU- 100 | 3.77 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 100 | 3.92 | 0 | Hydrophobic |
| N | N | LYS- 103 | 3.18 | 161.18 | H-Bond (Protein Donor) |
| N15 | O | LYS- 103 | 3.06 | 163.44 | H-Bond (Ligand Donor) |
| C2 | CB | LYS- 103 | 4.2 | 0 | Hydrophobic |
| C | CG2 | VAL- 106 | 4.13 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 106 | 4.45 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 106 | 4.42 | 0 | Hydrophobic |
| CL2 | CB | VAL- 106 | 4.22 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 106 | 4.04 | 0 | Hydrophobic |
| C17 | CG1 | VAL- 106 | 3.41 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 179 | 4 | 0 | Hydrophobic |
| CL | CD2 | TYR- 181 | 4.32 | 0 | Hydrophobic |
| CL2 | CD1 | TYR- 181 | 3.6 | 0 | Hydrophobic |
| CL | CD1 | TYR- 188 | 4.09 | 0 | Hydrophobic |
| CL2 | CB | TYR- 188 | 4.1 | 0 | Hydrophobic |
| C7 | CB | TYR- 188 | 3.45 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 188 | 3.86 | 0 | Aromatic Face/Face |
| C19 | CG | PRO- 225 | 3.89 | 0 | Hydrophobic |
| C20 | CB | PRO- 225 | 4.39 | 0 | Hydrophobic |
| C20 | CE2 | PHE- 227 | 3.43 | 0 | Hydrophobic |
| CL | CH2 | TRP- 229 | 3.82 | 0 | Hydrophobic |
| C10 | CB | TRP- 229 | 4.22 | 0 | Hydrophobic |
| C21 | CB | LEU- 234 | 4.17 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 234 | 3.68 | 0 | Hydrophobic |
| C20 | CG | PRO- 236 | 4.38 | 0 | Hydrophobic |
| C18 | CB | PRO- 236 | 3.74 | 0 | Hydrophobic |
| C13 | CE1 | TYR- 318 | 3.33 | 0 | Hydrophobic |
