sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2013-01-04
| Name: | Gag protein |
|---|---|
| ID: | A9PKC6_9HIV1 |
| AC: | A9PKC6 |
| Organism: | Human immunodeficiency virus 1 |
| Reign: | Viruses |
| TaxID: | 11676 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 28.833 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.710 | 732.375 |
| % Hydrophobic | % Polar |
|---|---|
| 63.13 | 36.87 |
| According to VolSite | |
| HET Code: | 1F6 |
|---|---|
| Formula: | C21H21F3N3O3 |
| Molecular weight: | 420.405 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 78.12 % |
| Polar Surface area: | 66.45 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 26.626 | 10.8884 | 38.4787 |
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 |
| F28 | CE2 | TRP- 23 | 3.54 | 0 | Hydrophobic |
| F26 | CZ2 | TRP- 23 | 3.65 | 0 | Hydrophobic |
| C17 | CG1 | VAL- 24 | 4.1 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 27 | 3.99 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 27 | 4.36 | 0 | Hydrophobic |
| C17 | CG1 | VAL- 27 | 3.9 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 27 | 4.43 | 0 | Hydrophobic |
| F28 | CG2 | VAL- 27 | 3.81 | 0 | Hydrophobic |
| C15 | CG | GLU- 28 | 3.74 | 0 | Hydrophobic |
| C17 | CG | GLU- 28 | 3.62 | 0 | Hydrophobic |
| C14 | CB | ALA- 31 | 3.98 | 0 | Hydrophobic |
| O29 | N | PHE- 32 | 2.8 | 134.46 | H-Bond (Protein Donor) |
| C23 | CG1 | VAL- 36 | 4.01 | 0 | Hydrophobic |
| F26 | CG1 | VAL- 36 | 3.73 | 0 | Hydrophobic |
| C22 | CB | VAL- 36 | 3.56 | 0 | Hydrophobic |
| C21 | CG1 | ILE- 37 | 4.08 | 0 | Hydrophobic |
| F27 | CD1 | PHE- 40 | 3.25 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 56 | 4.06 | 0 | Hydrophobic |
| F27 | CD2 | LEU- 56 | 3.6 | 0 | Hydrophobic |
| C17 | CG1 | VAL- 59 | 3.83 | 0 | Hydrophobic |
| F28 | CG2 | VAL- 59 | 3.46 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 59 | 3.82 | 0 | Hydrophobic |
| O30 | N | HIS- 62 | 2.94 | 159.1 | H-Bond (Protein Donor) |
| C5 | CD2 | LEU- 69 | 4.33 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 138 | 3.98 | 0 | Hydrophobic |
| C20 | CB | LEU- 138 | 4.06 | 0 | Hydrophobic |
| F26 | CD1 | LEU- 138 | 3.67 | 0 | Hydrophobic |
| F27 | CD1 | LEU- 138 | 3.77 | 0 | Hydrophobic |
| C1 | CD2 | LEU- 138 | 3.82 | 0 | Hydrophobic |
| C19 | CG2 | ILE- 141 | 3.71 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 142 | 3.21 | 0 | Hydrophobic |
