sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2011-08-17
| Name: | Envelope glycoprotein gp160 |
|---|---|
| ID: | C6G099_9HIV1 |
| AC: | C6G099 |
| Organism: | Human immunodeficiency virus 1 |
| Reign: | Viruses |
| TaxID: | 11676 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 39.129 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.421 | 256.500 |
| % Hydrophobic | % Polar |
|---|---|
| 43.42 | 56.58 |
| According to VolSite | |
| HET Code: | 03G |
|---|---|
| Formula: | C17H25ClN3O2 |
| Molecular weight: | 338.852 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.12 % |
| Polar Surface area: | 74.81 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -21.3852 | -2.89048 | 20.0358 |
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 | 4.13 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 255 | 3.22 | 0 | Hydrophobic |
| C3 | CG2 | THR- 257 | 4.13 | 0 | Hydrophobic |
| C3 | CB | GLU- 370 | 4.3 | 0 | Hydrophobic |
| C5 | CG | GLU- 370 | 4.21 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 371 | 4.27 | 0 | Hydrophobic |
| CL1 | CB | PHE- 376 | 4.48 | 0 | Hydrophobic |
| CL1 | CB | ASN- 377 | 3.8 | 0 | Hydrophobic |
| CL1 | CD2 | PHE- 382 | 3.87 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 424 | 3.25 | 0 | Hydrophobic |
| N1 | O | ASN- 425 | 2.9 | 133.2 | H-Bond (Ligand Donor) |
| C3 | CB | TRP- 427 | 4.47 | 0 | Hydrophobic |
| C13 | CB | TRP- 427 | 4.38 | 0 | Hydrophobic |
| C16 | CG2 | VAL- 430 | 3.86 | 0 | Hydrophobic |
| N2 | O | GLY- 473 | 3.34 | 127.84 | H-Bond (Ligand Donor) |
| C3 | CE | MET- 475 | 3.36 | 0 | Hydrophobic |
