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
2002-09-19
| 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 | 52 % |
| B | 48 % |
| B-Factor: | 24.366 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.989 | 729.000 |
| % Hydrophobic | % Polar |
|---|---|
| 48.15 | 51.85 |
| According to VolSite | |
| HET Code: | JE2 |
|---|---|
| Formula: | C32H37N3O5S |
| Molecular weight: | 575.718 g/mol |
| DrugBank ID: | DB02668 |
| Buried Surface Area: | 74.13 % |
| Polar Surface area: | 144.27 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 16.0667 | 23.0489 | 16.9758 |
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 |
| C19 | CD2 | LEU- 23 | 4.45 | 0 | Hydrophobic |
| C28 | CD2 | LEU- 23 | 3.47 | 0 | Hydrophobic |
| O23 | OD2 | ASP- 25 | 2.68 | 158.33 | H-Bond (Protein Donor) |
| O21 | OD1 | ASP- 25 | 2.6 | 157.6 | H-Bond (Ligand Donor) |
| O21 | OD2 | ASP- 25 | 3.16 | 125.44 | H-Bond (Ligand Donor) |
| N11 | O | GLY- 27 | 2.98 | 160.65 | H-Bond (Ligand Donor) |
| C8 | CB | ALA- 28 | 3.71 | 0 | Hydrophobic |
| C20 | CB | ALA- 28 | 4.35 | 0 | Hydrophobic |
| C7 | CB | ALA- 28 | 3.72 | 0 | Hydrophobic |
| C41 | CB | ALA- 28 | 3.64 | 0 | Hydrophobic |
| C3 | CB | ASP- 29 | 3.88 | 0 | Hydrophobic |
| C38 | CB | ASP- 29 | 4.26 | 0 | Hydrophobic |
| C1 | CB | ASP- 30 | 4.43 | 0 | Hydrophobic |
| C38 | CB | ASP- 30 | 3.66 | 0 | Hydrophobic |
| O2 | OD2 | ASP- 30 | 2.67 | 170.89 | H-Bond (Ligand Donor) |
| O2 | N | ASP- 30 | 3.45 | 138.38 | H-Bond (Protein Donor) |
| C8 | CG2 | VAL- 32 | 3.75 | 0 | Hydrophobic |
| C41 | CG2 | VAL- 32 | 3.61 | 0 | Hydrophobic |
| C37 | CG2 | VAL- 32 | 3.51 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 47 | 4.3 | 0 | Hydrophobic |
| C40 | CB | ILE- 47 | 3.7 | 0 | Hydrophobic |
| C36 | CD1 | ILE- 47 | 4.15 | 0 | Hydrophobic |
| C39 | CG2 | ILE- 47 | 3.67 | 0 | Hydrophobic |
| C8 | CG1 | ILE- 50 | 4.23 | 0 | Hydrophobic |
| S26 | CG1 | ILE- 50 | 4.08 | 0 | Hydrophobic |
| C16 | CB | ILE- 50 | 3.97 | 0 | Hydrophobic |
| C41 | CD1 | ILE- 50 | 3.91 | 0 | Hydrophobic |
| C38 | CD1 | LEU- 76 | 4.13 | 0 | Hydrophobic |
| C17 | CB | PRO- 81 | 3.7 | 0 | Hydrophobic |
| C16 | CG | PRO- 81 | 4.29 | 0 | Hydrophobic |
| C29 | CB | PRO- 81 | 4.11 | 0 | Hydrophobic |
| S26 | CG | PRO- 81 | 4.46 | 0 | Hydrophobic |
| C17 | CB | PHE- 82 | 3.72 | 0 | Hydrophobic |
| C18 | CG | PHE- 82 | 3.41 | 0 | Hydrophobic |
| C28 | CD1 | PHE- 82 | 3.72 | 0 | Hydrophobic |
| C28 | CG2 | VAL- 84 | 4 | 0 | Hydrophobic |
| S26 | CG2 | VAL- 84 | 4.39 | 0 | Hydrophobic |
| C41 | CG2 | VAL- 84 | 3.98 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 84 | 4.34 | 0 | Hydrophobic |
| N33 | O | HOH- 109 | 2.95 | 174.11 | H-Bond (Ligand Donor) |
