sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2007-07-02
| Name: | Protease |
|---|---|
| ID: | Q9J2P7_9HIV1 |
| AC: | Q9J2P7 |
| Organism: | Human immunodeficiency virus 1 |
| Reign: | Viruses |
| TaxID: | 11676 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 47 % |
| B | 53 % |
| B-Factor: | 24.337 |
|---|---|
| Number of residues: | 48 |
| Including | |
| Standard Amino Acids: | 47 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.047 | 884.250 |
| % Hydrophobic | % Polar |
|---|---|
| 41.98 | 58.02 |
| According to VolSite | |
| HET Code: | AB1 |
|---|---|
| Formula: | C37H48N4O5 |
| Molecular weight: | 628.801 g/mol |
| DrugBank ID: | DB01601 |
| Buried Surface Area: | 62.65 % |
| 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 |
|---|---|---|
| -13.3229 | 54.8692 | 4.48437 |
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 |
| C5 | CD2 | LEU- 23 | 4.44 | 0 | Hydrophobic |
| O4 | OD2 | ASP- 25 | 3.01 | 132.48 | H-Bond (Ligand Donor) |
| O4 | OD1 | ASP- 25 | 2.97 | 158.99 | H-Bond (Ligand Donor) |
| N3 | O | GLY- 27 | 3.09 | 153.5 | H-Bond (Ligand Donor) |
| C36 | CB | ALA- 28 | 3.83 | 0 | Hydrophobic |
| C14 | CB | ALA- 28 | 3.76 | 0 | Hydrophobic |
| N2 | OD2 | ASP- 29 | 2.73 | 158.36 | H-Bond (Ligand Donor) |
| O1 | N | ASP- 29 | 2.62 | 161.29 | H-Bond (Protein Donor) |
| C33 | CB | ASP- 29 | 3.68 | 0 | Hydrophobic |
| C15 | CB | ASP- 30 | 4.32 | 0 | Hydrophobic |
| C31 | CB | ASP- 30 | 3.42 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 32 | 3.89 | 0 | Hydrophobic |
| C36 | CB | VAL- 32 | 4.16 | 0 | Hydrophobic |
| C31 | CG2 | VAL- 32 | 4.08 | 0 | Hydrophobic |
| C27 | CG2 | ILE- 50 | 4.36 | 0 | Hydrophobic |
| C8 | CG1 | ILE- 50 | 3.57 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 50 | 3.67 | 0 | Hydrophobic |
| C7 | CG | PRO- 81 | 3.7 | 0 | Hydrophobic |
| C16 | CG | PRO- 81 | 3.45 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 82 | 3.76 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 82 | 4.02 | 0 | Hydrophobic |
| C14 | CG2 | ILE- 84 | 3.94 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 84 | 4.06 | 0 | Hydrophobic |
| C23 | CD1 | ILE- 84 | 4.34 | 0 | Hydrophobic |
| C36 | CG2 | ILE- 84 | 4.19 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 84 | 3.9 | 0 | Hydrophobic |
