sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 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 | 70 % |
| B | 30 % |
| B-Factor: | 19.760 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.399 | 799.875 |
| % Hydrophobic | % Polar |
|---|---|
| 51.05 | 48.95 |
| According to VolSite | |
| HET Code: | IM1 |
|---|---|
| Formula: | C31H42N4O4 |
| Molecular weight: | 534.690 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 39.29 % |
| 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 |
|---|---|---|
| -12.565 | 13.2629 | 35.6463 |
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 |
| C24 | CD1 | LEU- 23 | 3.74 | 0 | Hydrophobic |
| N39 | O | GLY- 27 | 2.77 | 158.54 | H-Bond (Ligand Donor) |
| C32 | CB | ALA- 28 | 4.48 | 0 | Hydrophobic |
| C19 | CB | ASP- 29 | 4.31 | 0 | Hydrophobic |
| O29 | N | ASP- 29 | 2.87 | 155.88 | H-Bond (Protein Donor) |
| C34 | CB | ASP- 30 | 4.04 | 0 | Hydrophobic |
| O5 | NZ | LYS- 45 | 3.11 | 141.08 | H-Bond (Protein Donor) |
| O7 | NZ | LYS- 45 | 3.02 | 131.73 | H-Bond (Protein Donor) |
| C17 | CG2 | ILE- 47 | 4.46 | 0 | Hydrophobic |
| C34 | CD1 | ILE- 47 | 3.87 | 0 | Hydrophobic |
| O18 | O | GLY- 48 | 3.21 | 145.08 | H-Bond (Ligand Donor) |
| N30 | O | GLY- 48 | 2.86 | 138.19 | H-Bond (Ligand Donor) |
| O18 | N | GLY- 48 | 3.12 | 148.09 | H-Bond (Protein Donor) |
| C26 | CG2 | ILE- 50 | 4.25 | 0 | Hydrophobic |
| C32 | CD1 | ILE- 50 | 4.17 | 0 | Hydrophobic |
| C24 | CG1 | VAL- 82 | 3.86 | 0 | Hydrophobic |
| C25 | CB | VAL- 82 | 3.96 | 0 | Hydrophobic |
