sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2012-05-29
| 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 | 100 % |
| B-Factor: | 30.258 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.959 | 344.250 |
| % Hydrophobic | % Polar |
|---|---|
| 58.82 | 41.18 |
| According to VolSite | |
| HET Code: | 0TQ |
|---|---|
| Formula: | C32H43N4O8S |
| Molecular weight: | 643.771 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 36.49 % |
| Polar Surface area: | 168.48 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 4 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| -8.95436 | 16.2371 | 28.3742 |
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 |
| C9 | CD2 | LEU- 23 | 4.06 | 0 | Hydrophobic |
| O3 | OD2 | ASP- 25 | 2.65 | 161.16 | H-Bond (Ligand Donor) |
| C32 | CB | ALA- 28 | 4.49 | 0 | Hydrophobic |
| C14 | CB | ALA- 28 | 4.31 | 0 | Hydrophobic |
| C30 | CB | ALA- 28 | 3.38 | 0 | Hydrophobic |
| O8 | OD2 | ASP- 30 | 2.54 | 136.11 | H-Bond (Protein Donor) |
| N3 | O | ASP- 30 | 2.92 | 141.47 | H-Bond (Ligand Donor) |
| C30 | CG2 | VAL- 32 | 3.58 | 0 | Hydrophobic |
| C38 | CG2 | ILE- 47 | 4.39 | 0 | Hydrophobic |
| C23 | CG1 | ILE- 50 | 4.47 | 0 | Hydrophobic |
| C12 | CG | PRO- 81 | 3.55 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 82 | 3.42 | 0 | Hydrophobic |
| C29 | CD1 | ILE- 84 | 3.63 | 0 | Hydrophobic |
| C7 | CD1 | ILE- 84 | 3.81 | 0 | Hydrophobic |
