sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
1995-03-29
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1B1 |
| AC: | P03366 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11678 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 49 % |
| B | 51 % |
| B-Factor: | 17.066 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.981 | 651.375 |
| % Hydrophobic | % Polar |
|---|---|
| 42.49 | 57.51 |
| According to VolSite | |
| HET Code: | GAN |
|---|---|
| Formula: | C32H53N5O5 |
| Molecular weight: | 587.794 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.49 % |
| Polar Surface area: | 145.67 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 5 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 14 |
| X | Y | Z |
|---|---|---|
| -8.50117 | 16.6072 | 27.0943 |
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 |
| C29 | CD1 | LEU- 23 | 4.32 | 0 | Hydrophobic |
| C8 | CB | ALA- 28 | 4.13 | 0 | Hydrophobic |
| C24 | CB | ALA- 28 | 3.91 | 0 | Hydrophobic |
| C38 | CB | ALA- 28 | 3.7 | 0 | Hydrophobic |
| O36 | N | ASP- 29 | 2.8 | 151.13 | H-Bond (Protein Donor) |
| N1 | OD2 | ASP- 30 | 3.82 | 0 | Ionic (Ligand Cationic) |
| C39 | CG2 | VAL- 32 | 3.99 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 47 | 4.18 | 0 | Hydrophobic |
| C42 | CG1 | ILE- 47 | 4.42 | 0 | Hydrophobic |
| C39 | CD1 | ILE- 47 | 3.34 | 0 | Hydrophobic |
| N6 | O | GLY- 48 | 2.95 | 158.61 | H-Bond (Ligand Donor) |
| C18 | CG2 | ILE- 50 | 4.47 | 0 | Hydrophobic |
| C20 | CG1 | ILE- 50 | 4.27 | 0 | Hydrophobic |
| C31 | CG2 | ILE- 50 | 3.97 | 0 | Hydrophobic |
| C39 | CG1 | ILE- 50 | 3.74 | 0 | Hydrophobic |
| C18 | CG | PRO- 81 | 3.72 | 0 | Hydrophobic |
| C16 | CG | PRO- 81 | 3.55 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 82 | 3.37 | 0 | Hydrophobic |
| C29 | CG2 | VAL- 82 | 3.8 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 84 | 3.81 | 0 | Hydrophobic |
| C24 | CD1 | ILE- 84 | 3.46 | 0 | Hydrophobic |
| C38 | CG2 | ILE- 84 | 4.04 | 0 | Hydrophobic |
| O33 | O | HOH- 501 | 2.88 | 167.85 | H-Bond (Protein Donor) |
