sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.310 Å
X-ray
2007-06-28
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1B5 |
| AC: | P04587 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11682 |
| EC Number: | 3.4.23.16 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 48 % |
| B | 52 % |
| B-Factor: | 27.125 |
|---|---|
| Number of residues: | 47 |
| Including | |
| Standard Amino Acids: | 46 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.729 | 742.500 |
| % Hydrophobic | % Polar |
|---|---|
| 36.82 | 63.18 |
| According to VolSite | |
| HET Code: | AB1 |
|---|---|
| Formula: | C37H48N4O5 |
| Molecular weight: | 628.801 g/mol |
| DrugBank ID: | DB01601 |
| Buried Surface Area: | 64.99 % |
| 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 |
|---|---|---|
| -13.0277 | 54.3469 | 4.33015 |
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 | 4.08 | 0 | Hydrophobic |
| O4 | OD2 | ASP- 25 | 2.78 | 151.32 | H-Bond (Protein Donor) |
| O4 | OD1 | ASP- 25 | 2.99 | 157.66 | H-Bond (Ligand Donor) |
| O4 | OD2 | ASP- 25 | 2.88 | 129.93 | H-Bond (Ligand Donor) |
| N3 | O | GLY- 27 | 2.94 | 157.84 | H-Bond (Ligand Donor) |
| C36 | CB | ALA- 28 | 3.9 | 0 | Hydrophobic |
| C14 | CB | ALA- 28 | 3.62 | 0 | Hydrophobic |
| N2 | OD1 | ASP- 29 | 2.86 | 163.47 | H-Bond (Ligand Donor) |
| O1 | N | ASP- 29 | 2.52 | 163.34 | H-Bond (Protein Donor) |
| C33 | CB | ASP- 29 | 3.69 | 0 | Hydrophobic |
| C15 | CB | ASP- 30 | 4.33 | 0 | Hydrophobic |
| C30 | CB | ASP- 30 | 4.19 | 0 | Hydrophobic |
| C31 | CB | ASP- 30 | 3.26 | 0 | Hydrophobic |
| C14 | CG2 | VAL- 32 | 4.38 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 32 | 3.82 | 0 | Hydrophobic |
| C30 | CG2 | VAL- 32 | 4.34 | 0 | Hydrophobic |
| C36 | CB | VAL- 32 | 4.41 | 0 | Hydrophobic |
| C9 | CG1 | ILE- 50 | 3.7 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 50 | 3.74 | 0 | Hydrophobic |
| C7 | CG | PRO- 81 | 3.71 | 0 | Hydrophobic |
| C16 | CG | PRO- 81 | 3.47 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 82 | 3.59 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 82 | 3.54 | 0 | Hydrophobic |
| C14 | CG2 | ILE- 84 | 3.83 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 84 | 4.01 | 0 | Hydrophobic |
| C23 | CD1 | ILE- 84 | 4.44 | 0 | Hydrophobic |
| C36 | CG2 | ILE- 84 | 4.41 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 84 | 3.66 | 0 | Hydrophobic |
| O2 | O | HOH- 201 | 3.48 | 179.95 | H-Bond (Protein Donor) |
