sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2007-11-26
| 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 | 49 % |
| B | 51 % |
| B-Factor: | 23.399 |
|---|---|
| Number of residues: | 50 |
| Including | |
| Standard Amino Acids: | 47 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.044 | 810.000 |
| % Hydrophobic | % Polar |
|---|---|
| 42.08 | 57.92 |
| According to VolSite | |
| HET Code: | LJH |
|---|---|
| Formula: | C30H36N5O4S2 |
| Molecular weight: | 594.768 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 77.18 % |
| Polar Surface area: | 160.16 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 14 |
| X | Y | Z |
|---|---|---|
| -12.0335 | 20.2749 | -17.2103 |
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 |
| C28 | CD2 | LEU- 23 | 4.05 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 23 | 3.9 | 0 | Hydrophobic |
| N1 | OD1 | ASP- 25 | 3.9 | 0 | Ionic (Ligand Cationic) |
| N1 | OD2 | ASP- 25 | 3.33 | 0 | Ionic (Ligand Cationic) |
| N1 | OD1 | ASP- 25 | 3.77 | 0 | Ionic (Ligand Cationic) |
| N1 | OD2 | ASP- 25 | 2.88 | 0 | Ionic (Ligand Cationic) |
| N1 | OD2 | ASP- 25 | 2.88 | 147.75 | H-Bond (Ligand Donor) |
| C3 | CB | ALA- 28 | 4.33 | 0 | Hydrophobic |
| C35 | CB | ALA- 28 | 3.39 | 0 | Hydrophobic |
| C20 | CB | ALA- 28 | 3.43 | 0 | Hydrophobic |
| N22 | O | ASP- 30 | 2.72 | 152.45 | H-Bond (Ligand Donor) |
| N39 | O | ASP- 30 | 2.94 | 146.54 | H-Bond (Ligand Donor) |
| C20 | CG1 | VAL- 32 | 3.7 | 0 | Hydrophobic |
| C35 | CG2 | VAL- 32 | 3.43 | 0 | Hydrophobic |
| C18 | CB | ILE- 47 | 3.89 | 0 | Hydrophobic |
| C19 | CD1 | ILE- 47 | 4.06 | 0 | Hydrophobic |
| C37 | CD1 | ILE- 47 | 4.05 | 0 | Hydrophobic |
| C13 | CG1 | ILE- 50 | 4.45 | 0 | Hydrophobic |
| C31 | CB | ILE- 50 | 3.88 | 0 | Hydrophobic |
| C30 | CG1 | ILE- 50 | 4.22 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 50 | 4.39 | 0 | Hydrophobic |
| C33 | CD1 | ILE- 50 | 3.42 | 0 | Hydrophobic |
| C11 | CB | PRO- 81 | 4.26 | 0 | Hydrophobic |
| C30 | CG | PRO- 81 | 4.07 | 0 | Hydrophobic |
| C13 | CG | PRO- 81 | 4.25 | 0 | Hydrophobic |
| C30 | CG1 | VAL- 82 | 4.45 | 0 | Hydrophobic |
| C29 | CG2 | VAL- 82 | 3.3 | 0 | Hydrophobic |
| C28 | CG1 | VAL- 82 | 3.29 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 82 | 3.57 | 0 | Hydrophobic |
| C21 | CD1 | ILE- 84 | 3.88 | 0 | Hydrophobic |
| C20 | CG2 | ILE- 84 | 4.49 | 0 | Hydrophobic |
| C12 | CG2 | ILE- 84 | 3.3 | 0 | Hydrophobic |
| C35 | CD1 | ILE- 84 | 3.3 | 0 | Hydrophobic |
| C29 | CD1 | ILE- 84 | 3.29 | 0 | Hydrophobic |
| C30 | CD1 | ILE- 84 | 3.41 | 0 | Hydrophobic |
