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
2011-06-02
| Name: | Protease |
|---|---|
| ID: | O38732_9HIV1 |
| AC: | O38732 |
| Organism: | Human immunodeficiency virus 1 |
| Reign: | Viruses |
| TaxID: | 11676 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 48 % |
| B | 52 % |
| B-Factor: | 21.683 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.007 | 769.500 |
| % Hydrophobic | % Polar |
|---|---|
| 45.61 | 54.39 |
| According to VolSite | |
| HET Code: | F72 |
|---|---|
| Formula: | C31H35N3O5S2 |
| Molecular weight: | 593.757 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 70.87 % |
| Polar Surface area: | 156.45 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 19.5437 | 30.7667 | 14.395 |
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 |
| C32 | CD1 | LEU- 23 | 4.48 | 0 | Hydrophobic |
| C33 | CD1 | LEU- 23 | 3.98 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 23 | 4.22 | 0 | Hydrophobic |
| O18 | OD1 | ASP- 25 | 2.6 | 169.62 | H-Bond (Ligand Donor) |
| O18 | OD2 | ASP- 25 | 2.94 | 122.19 | H-Bond (Ligand Donor) |
| O18 | OD1 | ASP- 25 | 2.55 | 170.17 | H-Bond (Protein Donor) |
| N20 | O | GLY- 27 | 3.22 | 158.47 | H-Bond (Ligand Donor) |
| C16 | CB | ALA- 28 | 4.39 | 0 | Hydrophobic |
| C27 | CB | ALA- 28 | 3.99 | 0 | Hydrophobic |
| C7 | CB | ALA- 28 | 3.36 | 0 | Hydrophobic |
| C25 | CB | ASP- 29 | 3.9 | 0 | Hydrophobic |
| O27 | OD2 | ASP- 30 | 2.99 | 166.84 | H-Bond (Ligand Donor) |
| N1 | N | ASP- 30 | 3.18 | 138.9 | H-Bond (Protein Donor) |
| C7 | CG2 | VAL- 32 | 3.7 | 0 | Hydrophobic |
| S1 | CB | ILE- 47 | 3.8 | 0 | Hydrophobic |
| C27 | CD1 | ILE- 50 | 3.79 | 0 | Hydrophobic |
| C20 | CG1 | ILE- 50 | 4.04 | 0 | Hydrophobic |
| C37 | CB | ILE- 50 | 4.19 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 50 | 4.13 | 0 | Hydrophobic |
| C18 | CG | PRO- 81 | 4.25 | 0 | Hydrophobic |
| C36 | CG | PRO- 81 | 3.85 | 0 | Hydrophobic |
| C11 | CB | VAL- 82 | 3.9 | 0 | Hydrophobic |
| C35 | CG1 | VAL- 82 | 3.55 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 84 | 4.29 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 84 | 3.89 | 0 | Hydrophobic |
| C37 | CD1 | ILE- 84 | 3.91 | 0 | Hydrophobic |
