sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.750 Å
X-ray
2007-05-07
| Name: | Protease |
|---|---|
| ID: | O38707_9HIV1 |
| AC: | O38707 |
| Organism: | Human immunodeficiency virus 1 |
| Reign: | Viruses |
| TaxID: | 11676 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 49 % |
| B | 51 % |
| B-Factor: | 17.132 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.668 | 644.625 |
| % Hydrophobic | % Polar |
|---|---|
| 42.93 | 57.07 |
| According to VolSite | |
| HET Code: | MUV |
|---|---|
| Formula: | C23H31N3O6S |
| Molecular weight: | 477.574 g/mol |
| DrugBank ID: | DB08223 |
| Buried Surface Area: | 71.92 % |
| Polar Surface area: | 137.32 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 19.6005 | 29.6639 | 13.8269 |
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 |
| C33 | CD1 | LEU- 23 | 4 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 23 | 4.48 | 0 | Hydrophobic |
| O18 | OD1 | ASP- 25 | 2.59 | 172.58 | H-Bond (Ligand Donor) |
| O18 | OD2 | ASP- 25 | 2.91 | 120.38 | H-Bond (Ligand Donor) |
| O18 | OD1 | ASP- 25 | 2.59 | 162.9 | H-Bond (Protein Donor) |
| N20 | O | GLY- 27 | 3.15 | 154.48 | H-Bond (Ligand Donor) |
| C23 | CB | ALA- 28 | 3.98 | 0 | Hydrophobic |
| C16 | CB | ALA- 28 | 4.17 | 0 | Hydrophobic |
| O26 | N | ASP- 29 | 2.82 | 139.36 | H-Bond (Protein Donor) |
| N27 | O | GLY- 48 | 3.02 | 154.24 | H-Bond (Ligand Donor) |
| C23 | CD1 | ILE- 50 | 3.82 | 0 | Hydrophobic |
| C37 | CB | ILE- 50 | 4.28 | 0 | Hydrophobic |
| C36 | CG | PRO- 81 | 3.61 | 0 | Hydrophobic |
| C15 | CG | PRO- 81 | 3.96 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 82 | 3.79 | 0 | Hydrophobic |
| C35 | CG2 | VAL- 82 | 3.6 | 0 | Hydrophobic |
| C37 | CD1 | ILE- 84 | 3.96 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 84 | 4.07 | 0 | Hydrophobic |
