sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.880 Å
X-ray
2011-05-20
| Name: | Protease |
|---|---|
| ID: | Q7SSI0_9HIV1 |
| AC: | Q7SSI0 |
| Organism: | Human immunodeficiency virus 1 |
| Reign: | Viruses |
| TaxID: | 11676 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 52 % |
| B | 48 % |
| B-Factor: | 13.601 |
|---|---|
| Number of residues: | 45 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.071 | 840.375 |
| % Hydrophobic | % Polar |
|---|---|
| 45.38 | 54.62 |
| According to VolSite | |
| HET Code: | ROC |
|---|---|
| Formula: | C38H51N6O5 |
| Molecular weight: | 671.849 g/mol |
| DrugBank ID: | DB01232 |
| Buried Surface Area: | 67.42 % |
| Polar Surface area: | 167.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 6 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 2.83 | 8.35563 | 38.4623 |
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 |
| CD2 | CD2 | LEU- 23 | 3.65 | 0 | Hydrophobic |
| O2 | OD2 | ASP- 25 | 2.51 | 150.06 | H-Bond (Ligand Donor) |
| O2 | OD1 | ASP- 25 | 2.7 | 160.74 | H-Bond (Protein Donor) |
| N2 | O | GLY- 27 | 3.22 | 169.99 | H-Bond (Ligand Donor) |
| CB | CB | ALA- 28 | 4.15 | 0 | Hydrophobic |
| C11 | CB | ALA- 28 | 4.22 | 0 | Hydrophobic |
| C22 | CB | ALA- 28 | 4.08 | 0 | Hydrophobic |
| O | N | ASP- 29 | 3.18 | 156.78 | H-Bond (Protein Donor) |
| OD1 | N | ASP- 30 | 2.9 | 149.2 | H-Bond (Protein Donor) |
| C11 | CB | ASP- 30 | 3.82 | 0 | Hydrophobic |
| CB | CD1 | ILE- 32 | 4.1 | 0 | Hydrophobic |
| C22 | CG2 | ILE- 32 | 4.06 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 47 | 4.19 | 0 | Hydrophobic |
| C32 | CG2 | VAL- 47 | 4.11 | 0 | Hydrophobic |
| N | O | GLY- 48 | 2.94 | 137.49 | H-Bond (Ligand Donor) |
| ND2 | O | GLY- 48 | 3.17 | 150.38 | H-Bond (Ligand Donor) |
| CB | CD1 | ILE- 50 | 4.49 | 0 | Hydrophobic |
| CD1 | CD1 | ILE- 50 | 4 | 0 | Hydrophobic |
| CE1 | CG1 | ILE- 50 | 4.18 | 0 | Hydrophobic |
| C71 | CB | ILE- 50 | 4.32 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 50 | 3.32 | 0 | Hydrophobic |
| C32 | CD1 | ILE- 50 | 3.44 | 0 | Hydrophobic |
| C61 | CB | ILE- 50 | 3.77 | 0 | Hydrophobic |
| C7 | CG | PRO- 81 | 3.82 | 0 | Hydrophobic |
| CZ | CG | PRO- 81 | 4.07 | 0 | Hydrophobic |
| C51 | CG | PRO- 81 | 3.4 | 0 | Hydrophobic |
| C3A | CD1 | ILE- 82 | 4.05 | 0 | Hydrophobic |
| C41 | CG1 | ILE- 82 | 3.67 | 0 | Hydrophobic |
| CE2 | CG2 | ILE- 82 | 3.76 | 0 | Hydrophobic |
| CB | CD1 | ILE- 84 | 4.05 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 84 | 3.77 | 0 | Hydrophobic |
| C7A | CG2 | ILE- 84 | 4.03 | 0 | Hydrophobic |
| CG1 | CD1 | ILE- 84 | 3.67 | 0 | Hydrophobic |
