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
2006-12-04
| Name: | Protease |
|---|---|
| ID: | Q5RZ08_9HIV1 |
| AC: | Q5RZ08 |
| Organism: | Human immunodeficiency virus 1 |
| Reign: | Viruses |
| TaxID: | 11676 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 56 % |
| B | 44 % |
| B-Factor: | 23.407 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 43 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.605 | 718.875 |
| % Hydrophobic | % Polar |
|---|---|
| 40.38 | 59.62 |
| According to VolSite | |
| HET Code: | TPV |
|---|---|
| Formula: | C31H32F3N2O5S |
| Molecular weight: | 601.656 g/mol |
| DrugBank ID: | DB00932 |
| Buried Surface Area: | 68.31 % |
| Polar Surface area: | 116.8 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| 11.689 | 19.2476 | 17.2066 |
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 |
| C18 | CD | ARG- 8 | 4.46 | 0 | Hydrophobic |
| F40 | CD | ARG- 8 | 3.39 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 23 | 4.3 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 23 | 3.64 | 0 | Hydrophobic |
| F40 | CD2 | LEU- 23 | 3.55 | 0 | Hydrophobic |
| O8 | OD1 | ASP- 25 | 3.12 | 135.51 | H-Bond (Ligand Donor) |
| O8 | OD1 | ASP- 25 | 3.34 | 141.73 | H-Bond (Ligand Donor) |
| C11 | CB | ALA- 28 | 3.94 | 0 | Hydrophobic |
| C25 | CB | ALA- 28 | 3.3 | 0 | Hydrophobic |
| N34 | N | ASP- 29 | 3.18 | 170.59 | H-Bond (Protein Donor) |
| O31 | N | ASP- 30 | 3.2 | 136.99 | H-Bond (Protein Donor) |
| C11 | CG2 | VAL- 32 | 3.86 | 0 | Hydrophobic |
| C25 | CG1 | VAL- 32 | 4.4 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 47 | 4.39 | 0 | Hydrophobic |
| C26 | CD1 | ILE- 47 | 4.28 | 0 | Hydrophobic |
| O7 | N | ILE- 50 | 3.04 | 173.97 | H-Bond (Protein Donor) |
| O7 | N | ILE- 50 | 2.85 | 149.49 | H-Bond (Protein Donor) |
| C11 | CG1 | ILE- 50 | 3.79 | 0 | Hydrophobic |
| C24 | CG2 | ILE- 50 | 3.89 | 0 | Hydrophobic |
| C27 | CD1 | ILE- 50 | 3.68 | 0 | Hydrophobic |
| F42 | CG | PRO- 81 | 4.41 | 0 | Hydrophobic |
| C15 | CG | PRO- 81 | 3.83 | 0 | Hydrophobic |
| F41 | CG1 | VAL- 82 | 3.54 | 0 | Hydrophobic |
| F42 | CG2 | VAL- 82 | 3.29 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 82 | 3.73 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 84 | 4.27 | 0 | Hydrophobic |
| C13 | CD1 | ILE- 84 | 4.31 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 84 | 3.77 | 0 | Hydrophobic |
| C25 | CD1 | ILE- 84 | 4.24 | 0 | Hydrophobic |
| O32 | O | HOH- 330 | 3.45 | 141.92 | H-Bond (Protein Donor) |
