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
2012-11-28
| Name: | Envelope glycoprotein gp160 |
|---|---|
| ID: | Q0ED31_9HIV1 |
| AC: | Q0ED31 |
| Organism: | Human immunodeficiency virus 1 |
| Reign: | Viruses |
| TaxID: | 11676 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 43.310 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.605 | 253.125 |
| % Hydrophobic | % Polar |
|---|---|
| 57.33 | 42.67 |
| According to VolSite | |
| HET Code: | 1C1 |
|---|---|
| Formula: | C19H20ClFN5O2 |
| Molecular weight: | 404.846 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.67 % |
| Polar Surface area: | 121.84 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -3.74761 | -14.8508 | -9.79132 |
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 |
| CL1 | CH2 | TRP- 112 | 4.48 | 0 | Hydrophobic |
| CL1 | CG1 | VAL- 255 | 4.31 | 0 | Hydrophobic |
| F23 | CG1 | VAL- 255 | 3.8 | 0 | Hydrophobic |
| F23 | CG2 | THR- 257 | 3.78 | 0 | Hydrophobic |
| C21 | CB | GLU- 370 | 4.32 | 0 | Hydrophobic |
| C27 | CG | GLU- 370 | 3.97 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 371 | 4.04 | 0 | Hydrophobic |
| F23 | CB | SER- 375 | 4.32 | 0 | Hydrophobic |
| CL1 | CB | ASN- 377 | 4.43 | 0 | Hydrophobic |
| CL1 | CD1 | PHE- 382 | 3.7 | 0 | Hydrophobic |
| C26 | CD1 | ILE- 424 | 3.66 | 0 | Hydrophobic |
| N19 | O | ASN- 425 | 2.89 | 132.08 | H-Bond (Ligand Donor) |
| N01 | O | MET- 426 | 3.18 | 138.28 | H-Bond (Ligand Donor) |
| N03 | O | MET- 426 | 2.94 | 142.39 | H-Bond (Ligand Donor) |
| C21 | CB | TRP- 427 | 3.99 | 0 | Hydrophobic |
| C27 | CB | TRP- 427 | 4.18 | 0 | Hydrophobic |
| N14 | O | GLY- 473 | 3.04 | 161.17 | H-Bond (Ligand Donor) |
