sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
1998-05-10
| 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 | 54 % |
| B | 46 % |
| B-Factor: | 17.710 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.930 | 648.000 |
| % Hydrophobic | % Polar |
|---|---|
| 46.88 | 53.13 |
| According to VolSite | |
| HET Code: | IM1 |
|---|---|
| Formula: | C31H42N4O4 |
| Molecular weight: | 534.690 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 67.94 % |
| Polar Surface area: | 116.34 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 14 |
| X | Y | Z |
|---|---|---|
| -9.07571 | 16.2986 | 27.2892 |
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 |
| C27 | CD2 | LEU- 23 | 4.42 | 0 | Hydrophobic |
| O18 | OD2 | ASP- 25 | 2.84 | 175.68 | H-Bond (Ligand Donor) |
| O18 | OD1 | ASP- 25 | 3.06 | 121.46 | H-Bond (Ligand Donor) |
| N8 | O | GLY- 27 | 2.86 | 165.59 | H-Bond (Ligand Donor) |
| N30 | O | GLY- 27 | 3.05 | 169.03 | H-Bond (Ligand Donor) |
| C32 | CB | ALA- 28 | 3.5 | 0 | Hydrophobic |
| C4 | CB | ALA- 28 | 3.6 | 0 | Hydrophobic |
| N39 | N | ASP- 29 | 3.45 | 149.26 | H-Bond (Protein Donor) |
| C4 | CB | ASP- 30 | 4.27 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 32 | 4.49 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 32 | 4.35 | 0 | Hydrophobic |
| C34 | CD1 | ILE- 32 | 3.92 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 47 | 4.2 | 0 | Hydrophobic |
| N36 | O | GLY- 48 | 2.67 | 129.28 | H-Bond (Ligand Donor) |
| C3 | CD1 | ILE- 50 | 3.75 | 0 | Hydrophobic |
| C15 | CG1 | ILE- 50 | 4.4 | 0 | Hydrophobic |
| C17 | CD1 | ILE- 50 | 4.32 | 0 | Hydrophobic |
| C34 | CD1 | ILE- 50 | 4.01 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 50 | 3.7 | 0 | Hydrophobic |
| C23 | CG2 | ILE- 50 | 3.79 | 0 | Hydrophobic |
| C15 | CG | PRO- 81 | 3.73 | 0 | Hydrophobic |
| C24 | CB | PRO- 81 | 3.7 | 0 | Hydrophobic |
| C22 | CG1 | ILE- 82 | 4.49 | 0 | Hydrophobic |
| C25 | CG1 | ILE- 82 | 3.95 | 0 | Hydrophobic |
| C26 | CD1 | ILE- 82 | 3.4 | 0 | Hydrophobic |
| C12 | CG2 | ILE- 82 | 3.59 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 84 | 4.37 | 0 | Hydrophobic |
| C21 | CD1 | ILE- 84 | 3.95 | 0 | Hydrophobic |
| C34 | CD1 | ILE- 84 | 3.9 | 0 | Hydrophobic |
