sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.550 Å
X-ray
2006-08-22
| Name: | Protease |
|---|---|
| ID: | Q903J0_9HIV1 |
| AC: | Q903J0 |
| 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: | 16.428 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 46 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.843 | 810.000 |
| % Hydrophobic | % Polar |
|---|---|
| 42.08 | 57.92 |
| According to VolSite | |
| HET Code: | KGQ |
|---|---|
| Formula: | C33H49N2O12PS |
| Molecular weight: | 728.787 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.06 % |
| Polar Surface area: | 186.58 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 20 |
| X | Y | Z |
|---|---|---|
| 14.5889 | 21.5261 | 15.6585 |
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 |
| C10 | CD2 | LEU- 23 | 4.29 | 0 | Hydrophobic |
| O8 | OD2 | ASP- 25 | 2.55 | 166.32 | H-Bond (Ligand Donor) |
| C20 | CB | ALA- 28 | 4.38 | 0 | Hydrophobic |
| C24 | CB | ALA- 28 | 3.5 | 0 | Hydrophobic |
| C31 | CB | ASP- 29 | 3.7 | 0 | Hydrophobic |
| O5 | N | ASP- 30 | 3.34 | 153.5 | H-Bond (Protein Donor) |
| C31 | CB | ASP- 30 | 4.32 | 0 | Hydrophobic |
| C25 | CG2 | VAL- 32 | 3.55 | 0 | Hydrophobic |
| C27 | CB | ILE- 47 | 4.15 | 0 | Hydrophobic |
| C26 | CD1 | ILE- 47 | 4.46 | 0 | Hydrophobic |
| C31 | CG2 | ILE- 47 | 3.8 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 50 | 4.01 | 0 | Hydrophobic |
| C31 | CD1 | LEU- 76 | 4.4 | 0 | Hydrophobic |
| C18 | CB | PRO- 81 | 3.8 | 0 | Hydrophobic |
| C13 | CG | PRO- 81 | 3.52 | 0 | Hydrophobic |
| C17 | CB | PRO- 81 | 4.19 | 0 | Hydrophobic |
| C13 | CB | VAL- 82 | 4.39 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 82 | 3.94 | 0 | Hydrophobic |
| C10 | CB | VAL- 82 | 4.38 | 0 | Hydrophobic |
| C14 | CG2 | VAL- 82 | 3.61 | 0 | Hydrophobic |
| C16 | CG2 | VAL- 82 | 3.78 | 0 | Hydrophobic |
| C8 | CG1 | VAL- 84 | 4.26 | 0 | Hydrophobic |
| C24 | CG2 | VAL- 84 | 4.42 | 0 | Hydrophobic |
| O8 | OD1 | ASP- 225 | 2.55 | 166.4 | H-Bond (Protein Donor) |
| N | O | GLY- 227 | 3.1 | 152.11 | H-Bond (Ligand Donor) |
| C3 | CB | ALA- 228 | 3.66 | 0 | Hydrophobic |
| C32 | CB | ASP- 229 | 3.89 | 0 | Hydrophobic |
| C2 | CB | ASP- 229 | 4.27 | 0 | Hydrophobic |
| O11 | N | ASP- 229 | 3.08 | 154.49 | H-Bond (Protein Donor) |
| O4 | N | ASP- 230 | 3.11 | 174.19 | H-Bond (Protein Donor) |
| C3 | CG2 | VAL- 232 | 4.01 | 0 | Hydrophobic |
| C11 | CB | ILE- 250 | 4.16 | 0 | Hydrophobic |
| C23 | CD1 | ILE- 250 | 4.09 | 0 | Hydrophobic |
| C18 | CZ | PHE- 253 | 3.79 | 0 | Hydrophobic |
| C19 | CE1 | PHE- 253 | 3.68 | 0 | Hydrophobic |
| C30 | CG | PRO- 281 | 3.24 | 0 | Hydrophobic |
| C29 | CG1 | VAL- 284 | 4.28 | 0 | Hydrophobic |
