sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2003-12-12
| Name: | Protease |
|---|---|
| ID: | Q9QM22_9HIV1 |
| AC: | Q9QM22 |
| Organism: | Human immunodeficiency virus 1 |
| Reign: | Viruses |
| TaxID: | 11676 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 55 % |
| B | 45 % |
| B-Factor: | 42.689 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.391 | 344.250 |
| % Hydrophobic | % Polar |
|---|---|
| 45.10 | 54.90 |
| According to VolSite | |
| HET Code: | AB1 |
|---|---|
| Formula: | C37H48N4O5 |
| Molecular weight: | 628.801 g/mol |
| DrugBank ID: | DB01601 |
| Buried Surface Area: | 37.38 % |
| Polar Surface area: | 120 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 15 |
| X | Y | Z |
|---|---|---|
| 15.0485 | 35.0539 | -0.0217609 |
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 |
| C15 | CD2 | LEU- 23 | 3.63 | 0 | Hydrophobic |
| O4 | ND2 | ASN- 25 | 3.42 | 150.68 | H-Bond (Protein Donor) |
| C4 | CB | ALA- 28 | 3.99 | 0 | Hydrophobic |
| C35 | CG2 | VAL- 32 | 4.43 | 0 | Hydrophobic |
| C16 | CG1 | ILE- 50 | 3.82 | 0 | Hydrophobic |
| C33 | CB | THR- 80 | 3.49 | 0 | Hydrophobic |
| C37 | CB | PRO- 81 | 3.57 | 0 | Hydrophobic |
| C17 | CG | PRO- 81 | 3.27 | 0 | Hydrophobic |
| C32 | CB | PRO- 81 | 3.59 | 0 | Hydrophobic |
| C33 | CG | PRO- 81 | 4.1 | 0 | Hydrophobic |
| C32 | CB | ALA- 82 | 4.13 | 0 | Hydrophobic |
| C33 | CG2 | VAL- 84 | 4.06 | 0 | Hydrophobic |
| C32 | CG2 | VAL- 84 | 3.7 | 0 | Hydrophobic |
