sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2011-07-21
| 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: | 47.918 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.626 | 486.000 |
| % Hydrophobic | % Polar |
|---|---|
| 70.83 | 29.17 |
| According to VolSite | |
| HET Code: | 5MA |
|---|---|
| Formula: | C20H15Cl3N7O |
| Molecular weight: | 475.738 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 80.95 % |
| Polar Surface area: | 109.15 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 8.71703 | 11.6521 | 16.8794 |
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 |
| CL2 | CB | PRO- 95 | 3.46 | 0 | Hydrophobic |
| C2 | CB | LEU- 100 | 4.37 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 100 | 4.07 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 100 | 4.43 | 0 | Hydrophobic |
| C14 | CB | LEU- 100 | 4.14 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 100 | 3.74 | 0 | Hydrophobic |
| N16 | N | LYS- 103 | 2.95 | 161.9 | H-Bond (Protein Donor) |
| N17 | O | LYS- 103 | 2.76 | 151.06 | H-Bond (Ligand Donor) |
| C1 | CD | LYS- 103 | 3.41 | 0 | Hydrophobic |
| CL3 | CG2 | VAL- 106 | 4.09 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 106 | 3.93 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 106 | 4.18 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 106 | 4.22 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 106 | 3.54 | 0 | Hydrophobic |
| CL3 | CG2 | VAL- 108 | 3.41 | 0 | Hydrophobic |
| CL1 | CB | VAL- 179 | 4.4 | 0 | Hydrophobic |
| CL1 | CD2 | TYR- 181 | 3.47 | 0 | Hydrophobic |
| CL2 | CD1 | TYR- 181 | 4.01 | 0 | Hydrophobic |
| C6 | CB | TYR- 181 | 4.32 | 0 | Hydrophobic |
| CL1 | CB | TYR- 188 | 3.95 | 0 | Hydrophobic |
| CL2 | CD1 | TYR- 188 | 4.46 | 0 | Hydrophobic |
| C5 | CB | TYR- 188 | 4.48 | 0 | Hydrophobic |
| C7 | CB | TYR- 188 | 3.3 | 0 | Hydrophobic |
| C8 | CB | TYR- 188 | 3.67 | 0 | Hydrophobic |
| C22 | CB | PRO- 225 | 3.96 | 0 | Hydrophobic |
| CL3 | CD2 | PHE- 227 | 3.67 | 0 | Hydrophobic |
| CL2 | CH2 | TRP- 229 | 3.94 | 0 | Hydrophobic |
| C23 | CB | LEU- 234 | 4.33 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 234 | 3.52 | 0 | Hydrophobic |
| C14 | CZ | TYR- 318 | 3.37 | 0 | Hydrophobic |
