sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.940 Å
X-ray
2012-02-23
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 50.658 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.743 | 246.375 |
| % Hydrophobic | % Polar |
|---|---|
| 60.27 | 39.73 |
| According to VolSite | |
| HET Code: | 0M1 |
|---|---|
| Formula: | C15H20ClFN3O4 |
| Molecular weight: | 360.788 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 53.32 % |
| Polar Surface area: | 104.3 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -9.63396 | -33.8961 | -0.160667 |
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 | 4.27 | 0 | Hydrophobic |
| F08 | CG1 | VAL- 255 | 3.77 | 0 | Hydrophobic |
| F08 | CG2 | THR- 257 | 3.83 | 0 | Hydrophobic |
| C03 | CG | GLU- 370 | 4.17 | 0 | Hydrophobic |
| C05 | CG | GLU- 370 | 3.85 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 371 | 3.69 | 0 | Hydrophobic |
| F08 | CB | SER- 375 | 3.99 | 0 | Hydrophobic |
| CL1 | CB | ASN- 377 | 4.42 | 0 | Hydrophobic |
| CL1 | CD1 | PHE- 382 | 3.81 | 0 | Hydrophobic |
| C06 | CD1 | ILE- 424 | 4.41 | 0 | Hydrophobic |
| N09 | O | ASN- 425 | 2.89 | 158.38 | H-Bond (Ligand Donor) |
| C03 | CB | TRP- 427 | 4.1 | 0 | Hydrophobic |
| C05 | CB | TRP- 427 | 4.4 | 0 | Hydrophobic |
| N12 | O | GLY- 473 | 3.32 | 137.35 | H-Bond (Ligand Donor) |
