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
2004-02-25
| 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 | 48 % |
| B | 52 % |
| B-Factor: | 19.737 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.048 | 820.125 |
| % Hydrophobic | % Polar |
|---|---|
| 45.68 | 54.32 |
| According to VolSite | |
| HET Code: | RIT |
|---|---|
| Formula: | C37H48N6O5S2 |
| Molecular weight: | 720.944 g/mol |
| DrugBank ID: | DB00503 |
| Buried Surface Area: | 55.55 % |
| Polar Surface area: | 202.26 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 18 |
| X | Y | Z |
|---|---|---|
| 18.4291 | 2.00706 | 11.8206 |
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 |
| S81 | CD2 | LEU- 23 | 4.21 | 0 | Hydrophobic |
| O41 | OD2 | ASP- 25 | 3.11 | 150.34 | H-Bond (Ligand Donor) |
| O41 | OD1 | ASP- 25 | 2.99 | 146.43 | H-Bond (Ligand Donor) |
| N58 | O | GLY- 27 | 3.13 | 153.3 | H-Bond (Ligand Donor) |
| C64 | CB | ALA- 28 | 3.94 | 0 | Hydrophobic |
| O76 | N | ASP- 29 | 3.35 | 153.8 | H-Bond (Protein Donor) |
| C68 | CB | ASP- 30 | 4.32 | 0 | Hydrophobic |
| C64 | CG1 | ILE- 32 | 4.03 | 0 | Hydrophobic |
| C68 | CD1 | ILE- 32 | 3.22 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 47 | 4.29 | 0 | Hydrophobic |
| C68 | CD1 | ILE- 47 | 3.95 | 0 | Hydrophobic |
| N20 | O | GLY- 48 | 3.21 | 154.37 | H-Bond (Ligand Donor) |
| C6 | CD1 | ILE- 50 | 3.78 | 0 | Hydrophobic |
| C31 | CG2 | ILE- 50 | 3.87 | 0 | Hydrophobic |
| C52 | CD1 | ILE- 50 | 3.29 | 0 | Hydrophobic |
| C62 | CD1 | ILE- 50 | 3.69 | 0 | Hydrophobic |
| C33 | CG | PRO- 81 | 3.47 | 0 | Hydrophobic |
| C50 | CG | PRO- 81 | 3.29 | 0 | Hydrophobic |
| S81 | CB | ALA- 82 | 4.33 | 0 | Hydrophobic |
| C85 | CB | ALA- 82 | 4.08 | 0 | Hydrophobic |
| C33 | CB | ALA- 82 | 4.14 | 0 | Hydrophobic |
| C49 | CB | ALA- 82 | 4 | 0 | Hydrophobic |
| C26 | CG2 | VAL- 84 | 4.28 | 0 | Hydrophobic |
| C44 | CG2 | VAL- 84 | 4.31 | 0 | Hydrophobic |
| C64 | CG1 | VAL- 84 | 4.5 | 0 | Hydrophobic |
