sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.850 Å
X-ray
2007-05-31
| Name: | Protease |
|---|---|
| ID: | O38710_9HIV1 |
| AC: | O38710 |
| Organism: | Human immunodeficiency virus 1 |
| Reign: | Viruses |
| TaxID: | 11676 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 51 % |
| B | 49 % |
| B-Factor: | 23.224 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.730 | 752.625 |
| % Hydrophobic | % Polar |
|---|---|
| 39.01 | 60.99 |
| According to VolSite | |
| HET Code: | MU1 |
|---|---|
| Formula: | C37H44N4O7 |
| Molecular weight: | 656.768 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.44 % |
| Polar Surface area: | 154.13 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 15 |
| X | Y | Z |
|---|---|---|
| 20.2967 | -2.91594 | 16.0413 |
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 |
| C19 | CD1 | LEU- 23 | 4.25 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 23 | 3.99 | 0 | Hydrophobic |
| O4 | OD1 | ASP- 25 | 2.73 | 121.48 | H-Bond (Ligand Donor) |
| O4 | OD2 | ASP- 25 | 2.79 | 166.56 | H-Bond (Ligand Donor) |
| O4 | OD2 | ASP- 25 | 2.58 | 140.22 | H-Bond (Protein Donor) |
| N3 | O | GLY- 27 | 2.99 | 158.54 | H-Bond (Ligand Donor) |
| N4 | O | GLY- 27 | 3.3 | 147.18 | H-Bond (Ligand Donor) |
| C27 | CB | ALA- 28 | 4.48 | 0 | Hydrophobic |
| C14 | CB | ALA- 28 | 3.74 | 0 | Hydrophobic |
| O1 | N | ASP- 29 | 2.94 | 172.13 | H-Bond (Protein Donor) |
| O30 | N | ASP- 29 | 2.75 | 165.39 | H-Bond (Protein Donor) |
| C38 | CB | ASP- 29 | 4.47 | 0 | Hydrophobic |
| C15 | CB | ASP- 30 | 4.34 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 32 | 3.94 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 47 | 4.27 | 0 | Hydrophobic |
| N1 | O | GLY- 48 | 3.06 | 168.32 | H-Bond (Ligand Donor) |
| C9 | CG1 | ILE- 50 | 4.36 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 50 | 3.49 | 0 | Hydrophobic |
| C16 | CG | PRO- 81 | 3.82 | 0 | Hydrophobic |
| C17 | CB | PRO- 81 | 4.42 | 0 | Hydrophobic |
| C7 | CB | PRO- 81 | 3.95 | 0 | Hydrophobic |
| C8 | CG | PRO- 81 | 3.73 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 82 | 4.03 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 82 | 3.86 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 84 | 3.71 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 84 | 3.72 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 84 | 3.81 | 0 | Hydrophobic |
