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
1998-01-22
| 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 | 50 % |
| B | 50 % |
| B-Factor: | 29.755 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.633 | 698.625 |
| % Hydrophobic | % Polar |
|---|---|
| 42.51 | 57.49 |
| According to VolSite | |
| HET Code: | MK1 |
|---|---|
| Formula: | C36H48N5O4 |
| Molecular weight: | 614.797 g/mol |
| DrugBank ID: | DB00224 |
| Buried Surface Area: | 63.35 % |
| Polar Surface area: | 119.23 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 5 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| 13.198 | 23.2807 | 5.60107 |
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 |
| C16 | CD2 | LEU- 23 | 3.57 | 0 | Hydrophobic |
| O2 | OD2 | ASP- 25 | 2.89 | 154.14 | H-Bond (Ligand Donor) |
| O2 | OD1 | ASP- 25 | 2.78 | 137.51 | H-Bond (Ligand Donor) |
| N4 | O | GLY- 27 | 3.02 | 172.92 | H-Bond (Ligand Donor) |
| O4 | O | GLY- 27 | 3.25 | 157.29 | H-Bond (Ligand Donor) |
| C5 | CB | ALA- 28 | 4.19 | 0 | Hydrophobic |
| C6 | CB | ALA- 28 | 3.86 | 0 | Hydrophobic |
| C29 | CB | ALA- 28 | 3.53 | 0 | Hydrophobic |
| O4 | N | ASP- 29 | 2.9 | 170.26 | H-Bond (Protein Donor) |
| C24 | CB | ASP- 29 | 4.38 | 0 | Hydrophobic |
| C5 | CB | ASP- 30 | 4.14 | 0 | Hydrophobic |
| C26 | CB | ASP- 30 | 4.03 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 32 | 4.5 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 32 | 3.98 | 0 | Hydrophobic |
| C27 | CG2 | VAL- 32 | 3.26 | 0 | Hydrophobic |
| C7 | CD1 | ILE- 47 | 4.21 | 0 | Hydrophobic |
| C27 | CD1 | ILE- 47 | 3.62 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 50 | 4.08 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 50 | 4.42 | 0 | Hydrophobic |
| C29 | CG1 | ILE- 50 | 4.13 | 0 | Hydrophobic |
| C19 | CG | PRO- 81 | 4.15 | 0 | Hydrophobic |
| C32 | CG | PRO- 81 | 3.24 | 0 | Hydrophobic |
| C32 | CG2 | VAL- 82 | 4.47 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 82 | 3.76 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 84 | 3.82 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 84 | 3.32 | 0 | Hydrophobic |
