sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2005-09-29
| Name: | Pol polyprotein |
|---|---|
| ID: | Q7SMT3_9HIV1 |
| AC: | Q7SMT3 |
| Organism: | Human immunodeficiency virus 1 |
| Reign: | Viruses |
| TaxID: | 11676 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 51 % |
| B | 49 % |
| B-Factor: | 14.655 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.039 | 742.500 |
| % Hydrophobic | % Polar |
|---|---|
| 45.91 | 54.09 |
| According to VolSite | |
| HET Code: | RIT |
|---|---|
| Formula: | C37H48N6O5S2 |
| Molecular weight: | 720.944 g/mol |
| DrugBank ID: | DB00503 |
| Buried Surface Area: | 58.54 % |
| 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 |
|---|---|---|
| 7.36496 | 16.7179 | 10.4882 |
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 | CD | ARG- 8 | 4.24 | 0 | Hydrophobic |
| C31 | CD2 | LEU- 23 | 4.15 | 0 | Hydrophobic |
| O41 | OD1 | ASP- 25 | 2.97 | 131.72 | H-Bond (Ligand Donor) |
| N11 | O | GLY- 27 | 2.99 | 156.64 | H-Bond (Ligand Donor) |
| N58 | O | GLY- 27 | 3.26 | 163.93 | H-Bond (Ligand Donor) |
| S3 | CB | ALA- 28 | 4.19 | 0 | Hydrophobic |
| C68 | CB | ALA- 28 | 3.9 | 0 | Hydrophobic |
| O76 | N | ASP- 29 | 3.31 | 157.13 | H-Bond (Protein Donor) |
| S3 | CB | ASP- 30 | 4.11 | 0 | Hydrophobic |
| C64 | CB | ASP- 30 | 4.36 | 0 | Hydrophobic |
| C68 | CG2 | ILE- 32 | 4.43 | 0 | Hydrophobic |
| S3 | CG2 | ILE- 47 | 3.9 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 47 | 3.81 | 0 | Hydrophobic |
| C62 | CG2 | ILE- 47 | 4.45 | 0 | Hydrophobic |
| C64 | CG1 | ILE- 47 | 4.43 | 0 | Hydrophobic |
| N20 | O | GLY- 48 | 3.23 | 165.44 | H-Bond (Ligand Donor) |
| C35 | CD1 | ILE- 50 | 4.23 | 0 | Hydrophobic |
| C68 | CD1 | ILE- 50 | 4.37 | 0 | Hydrophobic |
| C52 | CG1 | ILE- 50 | 4.09 | 0 | Hydrophobic |
| C90 | CB | PRO- 81 | 3.83 | 0 | Hydrophobic |
| C33 | CB | PRO- 81 | 4.16 | 0 | Hydrophobic |
| C51 | CG | PRO- 81 | 3.27 | 0 | Hydrophobic |
| S81 | CB | ALA- 82 | 4.13 | 0 | Hydrophobic |
| C49 | CB | ALA- 82 | 3.82 | 0 | Hydrophobic |
| C33 | CB | ALA- 82 | 3.8 | 0 | Hydrophobic |
| C68 | CD1 | ILE- 84 | 3.99 | 0 | Hydrophobic |
| C26 | CD1 | ILE- 84 | 3.26 | 0 | Hydrophobic |
| C44 | CD1 | ILE- 84 | 3.78 | 0 | Hydrophobic |
