sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2011-07-25
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1BR |
| AC: | P03367 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11686 |
| EC Number: | 3.4.23.16 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 49 % |
| B | 51 % |
| B-Factor: | 38.447 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.040 | 830.250 |
| % Hydrophobic | % Polar |
|---|---|
| 41.87 | 58.13 |
| According to VolSite | |
| HET Code: | 017 |
|---|---|
| Formula: | C27H37N3O7S |
| Molecular weight: | 547.664 g/mol |
| DrugBank ID: | DB01264 |
| Buried Surface Area: | 67.16 % |
| Polar Surface area: | 148.79 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| -1.97547 | -2.57971 | -21.6308 |
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 | 4.09 | 0 | Hydrophobic |
| C33 | CD2 | LEU- 23 | 4.32 | 0 | Hydrophobic |
| O18 | OD1 | ASP- 25 | 2.88 | 126.74 | H-Bond (Ligand Donor) |
| O18 | OD2 | ASP- 25 | 2.69 | 156.96 | H-Bond (Ligand Donor) |
| O18 | OD1 | ASP- 25 | 2.56 | 165.26 | H-Bond (Protein Donor) |
| N20 | O | GLY- 27 | 3.15 | 160.9 | H-Bond (Ligand Donor) |
| C16 | CB | ALA- 28 | 4.41 | 0 | Hydrophobic |
| C25 | CB | ALA- 28 | 3.87 | 0 | Hydrophobic |
| C3 | CB | ALA- 28 | 3.33 | 0 | Hydrophobic |
| C27 | CB | ASP- 29 | 4.11 | 0 | Hydrophobic |
| C29 | CB | ASP- 29 | 4.48 | 0 | Hydrophobic |
| O28 | N | ASP- 29 | 2.99 | 157.54 | H-Bond (Protein Donor) |
| N1 | O | ASP- 30 | 3.08 | 152.66 | H-Bond (Ligand Donor) |
| C25 | CB | ASP- 30 | 4.17 | 0 | Hydrophobic |
| C27 | CB | ASP- 30 | 4.33 | 0 | Hydrophobic |
| O26 | N | ASP- 30 | 3.15 | 145.74 | H-Bond (Protein Donor) |
| C25 | CG2 | VAL- 32 | 3.75 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 32 | 3.6 | 0 | Hydrophobic |
| C7 | CB | ILE- 47 | 4 | 0 | Hydrophobic |
| C25 | CD1 | ILE- 47 | 4.26 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 47 | 4.19 | 0 | Hydrophobic |
| C14 | CG1 | ILE- 50 | 4.24 | 0 | Hydrophobic |
| C37 | CB | ILE- 50 | 4.36 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 50 | 4.03 | 0 | Hydrophobic |
| C24 | CD1 | ILE- 50 | 3.92 | 0 | Hydrophobic |
| C36 | CG | PRO- 81 | 3.72 | 0 | Hydrophobic |
| C15 | CB | ALA- 82 | 4.02 | 0 | Hydrophobic |
| C34 | CB | ALA- 82 | 3.63 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 84 | 4.24 | 0 | Hydrophobic |
| C32 | CG1 | VAL- 84 | 4.45 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 84 | 3.92 | 0 | Hydrophobic |
