sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2002-09-18
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1BR |
| AC: | P03367 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11686 |
| EC Number: | 3.4.23.16 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 51 % |
| B | 49 % |
| B-Factor: | 24.455 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.788 | 658.125 |
| % Hydrophobic | % Polar |
|---|---|
| 44.62 | 55.38 |
| According to VolSite | |
| HET Code: | K57 |
|---|---|
| Formula: | C28H37N3O5S |
| Molecular weight: | 527.675 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.4 % |
| Polar Surface area: | 144.27 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 15.8904 | 22.3045 | 17.5828 |
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 | 3.52 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 23 | 3.76 | 0 | Hydrophobic |
| O26 | OD2 | ASP- 25 | 2.54 | 138.26 | H-Bond (Protein Donor) |
| O25 | OD1 | ASP- 25 | 2.68 | 136.72 | H-Bond (Protein Donor) |
| N9 | O | GLY- 27 | 3.22 | 168.02 | H-Bond (Ligand Donor) |
| C7 | CB | ALA- 28 | 3.72 | 0 | Hydrophobic |
| C35 | CB | ALA- 28 | 4.33 | 0 | Hydrophobic |
| C67 | CB | ALA- 28 | 4.26 | 0 | Hydrophobic |
| C5 | CB | ALA- 28 | 3.82 | 0 | Hydrophobic |
| C1 | CB | ASP- 29 | 3.81 | 0 | Hydrophobic |
| O33 | OD2 | ASP- 30 | 2.69 | 169.67 | H-Bond (Ligand Donor) |
| O33 | N | ASP- 30 | 3.44 | 137.65 | H-Bond (Protein Donor) |
| C35 | CB | ASP- 30 | 4.34 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 32 | 3.95 | 0 | Hydrophobic |
| C67 | CG2 | VAL- 32 | 4.14 | 0 | Hydrophobic |
| C7 | CD1 | ILE- 47 | 4.4 | 0 | Hydrophobic |
| C71 | CB | ILE- 47 | 3.99 | 0 | Hydrophobic |
| C6 | CB | ILE- 47 | 4.22 | 0 | Hydrophobic |
| C7 | CG1 | ILE- 50 | 3.76 | 0 | Hydrophobic |
| S17 | CG1 | ILE- 50 | 4.38 | 0 | Hydrophobic |
| C67 | CD1 | ILE- 50 | 4.06 | 0 | Hydrophobic |
| C71 | CG2 | ILE- 50 | 4.08 | 0 | Hydrophobic |
| C21 | CB | PRO- 81 | 4.03 | 0 | Hydrophobic |
| S17 | CG | PRO- 81 | 3.57 | 0 | Hydrophobic |
| C27 | CG2 | VAL- 82 | 3.94 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 82 | 3.49 | 0 | Hydrophobic |
| C7 | CD1 | ILE- 84 | 4.13 | 0 | Hydrophobic |
| S17 | CD1 | ILE- 84 | 4.02 | 0 | Hydrophobic |
| C67 | CD1 | ILE- 84 | 4.09 | 0 | Hydrophobic |
| C19 | CD1 | ILE- 84 | 3.72 | 0 | Hydrophobic |
| N30 | O | HOH- 1004 | 2.79 | 162.05 | H-Bond (Ligand Donor) |
