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: | C6G099_9HIV1 |
| AC: | C6G099 |
| Organism: | Human immunodeficiency virus 1 |
| Reign: | Viruses |
| TaxID: | 11676 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 22.278 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.714 | 472.500 |
| % Hydrophobic | % Polar |
|---|---|
| 51.43 | 48.57 |
| According to VolSite | |
| HET Code: | 1C1 |
|---|---|
| Formula: | C19H20ClFN5O2 |
| Molecular weight: | 404.846 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.06 % |
| 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 |
|---|---|---|
| -13.9905 | -57.6701 | 17.7087 |
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 | 4.25 | 0 | Hydrophobic |
| C24 | CG1 | VAL- 255 | 3.63 | 0 | Hydrophobic |
| F23 | CG2 | THR- 257 | 3.73 | 0 | Hydrophobic |
| C21 | CG | GLU- 370 | 3.98 | 0 | Hydrophobic |
| C27 | CG | GLU- 370 | 3.95 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 371 | 4.1 | 0 | Hydrophobic |
| F23 | CB | SER- 375 | 4.1 | 0 | Hydrophobic |
| CL1 | CB | ASN- 377 | 4.49 | 0 | Hydrophobic |
| CL1 | CD2 | PHE- 382 | 3.78 | 0 | Hydrophobic |
| C27 | CG2 | ILE- 424 | 3.61 | 0 | Hydrophobic |
| N19 | O | ASN- 425 | 2.73 | 161.12 | H-Bond (Ligand Donor) |
| N03 | O | MET- 426 | 3.01 | 121.75 | H-Bond (Ligand Donor) |
| C21 | CB | TRP- 427 | 4.19 | 0 | Hydrophobic |
| C27 | CB | TRP- 427 | 4.28 | 0 | Hydrophobic |
| C04 | CG2 | VAL- 430 | 4.25 | 0 | Hydrophobic |
| N14 | O | GLY- 473 | 3.24 | 172.11 | H-Bond (Ligand Donor) |
| C08 | CB | ASP- 474 | 4.14 | 0 | Hydrophobic |
| F23 | CE | MET- 475 | 3.34 | 0 | Hydrophobic |
