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
2009-02-27
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1B1 |
| AC: | P03366 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11678 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| G | 50 % |
| H | 50 % |
| B-Factor: | 24.491 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.126 | 958.500 |
| % Hydrophobic | % Polar |
|---|---|
| 44.37 | 55.63 |
| According to VolSite | |
| HET Code: | GGW |
|---|---|
| Formula: | C39H53N5O7 |
| Molecular weight: | 703.867 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.86 % |
| Polar Surface area: | 167.97 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 18 |
| X | Y | Z |
|---|---|---|
| 28.6072 | 4.74804 | -0.744588 |
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 |
| C21 | CD2 | LEU- 23 | 4.01 | 0 | Hydrophobic |
| C35 | CD2 | LEU- 23 | 4.37 | 0 | Hydrophobic |
| C37 | CD2 | LEU- 23 | 4.38 | 0 | Hydrophobic |
| O13 | OD1 | ASP- 25 | 3 | 123.15 | H-Bond (Ligand Donor) |
| O13 | OD2 | ASP- 25 | 2.68 | 167 | H-Bond (Ligand Donor) |
| N9 | O | GLY- 27 | 3.07 | 151.69 | H-Bond (Ligand Donor) |
| N22 | O | GLY- 27 | 3.05 | 142.34 | H-Bond (Ligand Donor) |
| C33 | CB | ALA- 28 | 3.79 | 0 | Hydrophobic |
| C50 | CB | ALA- 28 | 3.74 | 0 | Hydrophobic |
| C1 | CB | ASP- 29 | 4.17 | 0 | Hydrophobic |
| O4 | N | ASP- 29 | 2.95 | 176.84 | H-Bond (Protein Donor) |
| O28 | N | ASP- 29 | 3.14 | 169.94 | H-Bond (Protein Donor) |
| C51 | CB | ASP- 30 | 4.45 | 0 | Hydrophobic |
| C33 | CG2 | VAL- 32 | 4.45 | 0 | Hydrophobic |
| C50 | CG1 | VAL- 32 | 4.37 | 0 | Hydrophobic |
| C34 | CD1 | ILE- 47 | 3.98 | 0 | Hydrophobic |
| C49 | CD1 | ILE- 47 | 3.91 | 0 | Hydrophobic |
| C51 | CD1 | ILE- 47 | 4.46 | 0 | Hydrophobic |
| N5 | O | GLY- 48 | 2.99 | 168.63 | H-Bond (Ligand Donor) |
| N26 | O | GLY- 48 | 2.76 | 156.47 | H-Bond (Ligand Donor) |
| C17 | CD1 | ILE- 50 | 4.26 | 0 | Hydrophobic |
| C32 | CG1 | ILE- 50 | 4.03 | 0 | Hydrophobic |
| C34 | CG1 | ILE- 50 | 3.68 | 0 | Hydrophobic |
| C41 | CG1 | ILE- 50 | 4.43 | 0 | Hydrophobic |
| C49 | CG1 | ILE- 50 | 3.96 | 0 | Hydrophobic |
| C50 | CD1 | ILE- 50 | 4.42 | 0 | Hydrophobic |
| C45 | CB | PRO- 81 | 4.13 | 0 | Hydrophobic |
| C18 | CG | PRO- 81 | 3.7 | 0 | Hydrophobic |
| C40 | CG | PRO- 81 | 3.75 | 0 | Hydrophobic |
| C43 | CG | PRO- 81 | 3.63 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 82 | 3.66 | 0 | Hydrophobic |
| C36 | CG2 | VAL- 82 | 3.93 | 0 | Hydrophobic |
| C32 | CD1 | ILE- 84 | 3.84 | 0 | Hydrophobic |
| C35 | CD1 | ILE- 84 | 4.06 | 0 | Hydrophobic |
| C41 | CD1 | ILE- 84 | 4.49 | 0 | Hydrophobic |
| C50 | CD1 | ILE- 84 | 4.03 | 0 | Hydrophobic |
| C17 | CD1 | ILE- 84 | 4.04 | 0 | Hydrophobic |
