sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.230 Å
X-ray
2012-01-23
| 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 | 51 % |
| B | 49 % |
| B-Factor: | 14.529 |
|---|---|
| Number of residues: | 49 |
| Including | |
| Standard Amino Acids: | 45 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.760 | 759.375 |
| % Hydrophobic | % Polar |
|---|---|
| 37.78 | 62.22 |
| According to VolSite | |
| HET Code: | 0JV |
|---|---|
| Formula: | C31H43N3O9S |
| Molecular weight: | 633.753 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.66 % |
| Polar Surface area: | 161.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 15 |
| X | Y | Z |
|---|---|---|
| 15.4754 | 22.048 | 16.4524 |
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 | 3.9 | 0 | Hydrophobic |
| C33 | CD2 | LEU- 23 | 4.15 | 0 | Hydrophobic |
| O18 | OD2 | ASP- 25 | 2.62 | 153.24 | H-Bond (Ligand Donor) |
| O18 | OD1 | ASP- 25 | 2.7 | 129.88 | H-Bond (Ligand Donor) |
| O18 | OD1 | ASP- 25 | 2.89 | 143.46 | H-Bond (Protein Donor) |
| N20 | O | GLY- 27 | 3.3 | 154.6 | H-Bond (Ligand Donor) |
| C16 | CB | ALA- 28 | 4.13 | 0 | Hydrophobic |
| C25 | CB | ALA- 28 | 4.39 | 0 | Hydrophobic |
| C4 | CB | ALA- 28 | 3.43 | 0 | Hydrophobic |
| C40 | CB | ASP- 29 | 4.15 | 0 | Hydrophobic |
| C26 | CB | ASP- 29 | 4.19 | 0 | Hydrophobic |
| C28 | CB | ASP- 29 | 4.15 | 0 | Hydrophobic |
| O27 | N | ASP- 29 | 2.84 | 170.23 | H-Bond (Protein Donor) |
| O39 | N | ASP- 30 | 3.3 | 133.06 | H-Bond (Protein Donor) |
| C40 | CB | ASP- 30 | 4.01 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 32 | 3.98 | 0 | Hydrophobic |
| C40 | CG2 | ILE- 47 | 3.85 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 47 | 4.37 | 0 | Hydrophobic |
| C7 | CB | ILE- 47 | 4.29 | 0 | Hydrophobic |
| C25 | CD1 | ILE- 47 | 4.26 | 0 | Hydrophobic |
| C30 | CB | ILE- 47 | 4.05 | 0 | Hydrophobic |
| N41 | O | GLY- 48 | 2.77 | 167 | H-Bond (Ligand Donor) |
| C14 | CG1 | ILE- 50 | 4.25 | 0 | Hydrophobic |
| C24 | CD1 | ILE- 50 | 4.29 | 0 | Hydrophobic |
| C37 | CB | ILE- 50 | 4.4 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 50 | 3.83 | 0 | Hydrophobic |
| C35 | CB | PRO- 81 | 3.97 | 0 | Hydrophobic |
| C36 | CG | PRO- 81 | 3.98 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 82 | 3.55 | 0 | Hydrophobic |
| C45 | CG2 | VAL- 82 | 3.68 | 0 | Hydrophobic |
| C34 | CG2 | VAL- 82 | 3.6 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 84 | 4.24 | 0 | Hydrophobic |
| C37 | CD1 | ILE- 84 | 3.9 | 0 | Hydrophobic |
| O22 | O | HOH- 1001 | 3 | 179.96 | H-Bond (Protein Donor) |
| O23 | O | HOH- 1074 | 3.1 | 133.22 | H-Bond (Protein Donor) |
