sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2010-06-09
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1N5 |
| AC: | P12497 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11698 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 47 % |
| B | 53 % |
| B-Factor: | 30.248 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.688 | 486.000 |
| % Hydrophobic | % Polar |
|---|---|
| 49.31 | 50.69 |
| According to VolSite | |
| HET Code: | CDQ |
|---|---|
| Formula: | C18H13ClNO5 |
| Molecular weight: | 358.753 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.13 % |
| Polar Surface area: | 78.9 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 17.6048 | -15.6619 | 1.34768 |
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 |
| C6 | CG | PRO- 58 | 4.48 | 0 | Hydrophobic |
| CL25 | CG | PRO- 58 | 3.98 | 0 | Hydrophobic |
| C23 | CE1 | TYR- 83 | 4.08 | 0 | Hydrophobic |
| C14 | CG | PRO- 109 | 3.72 | 0 | Hydrophobic |
| C16 | CB | PRO- 109 | 4.22 | 0 | Hydrophobic |
| C2 | CB | PRO- 109 | 3.54 | 0 | Hydrophobic |
| C23 | CB | ASN- 184 | 4.11 | 0 | Hydrophobic |
| O19 | OG | SER- 195 | 2.54 | 154.9 | H-Bond (Protein Donor) |
| C12 | CB | GLU- 198 | 4.35 | 0 | Hydrophobic |
| C14 | CG2 | VAL- 201 | 4.17 | 0 | Hydrophobic |
| C13 | CG2 | ILE- 204 | 4.19 | 0 | Hydrophobic |
| C7 | CG2 | ILE- 204 | 3.54 | 0 | Hydrophobic |
| C7 | CB | ASP- 207 | 4.02 | 0 | Hydrophobic |
