sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.500 Å
X-ray
2011-07-23
| Name: | Avidin/streptavidin |
|---|---|
| ID: | Q12QS6_SHEDO |
| AC: | Q12QS6 |
| Organism: | Shewanella denitrificans |
| Reign: | Bacteria |
| TaxID: | 318161 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 22.389 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.306 | 357.750 |
| % Hydrophobic | % Polar |
|---|---|
| 48.11 | 51.89 |
| According to VolSite | |
| HET Code: | BTN |
|---|---|
| Formula: | C10H15N2O3S |
| Molecular weight: | 243.303 g/mol |
| DrugBank ID: | DB00121 |
| Buried Surface Area: | 69.41 % |
| Polar Surface area: | 106.55 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -7.67712 | -25.9103 | 0.7175 |
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 |
| O3 | ND2 | ASN- 15 | 2.88 | 149.97 | H-Bond (Protein Donor) |
| O3 | OG | SER- 19 | 2.59 | 136.45 | H-Bond (Protein Donor) |
| O3 | OH | TYR- 36 | 2.63 | 174.67 | H-Bond (Protein Donor) |
| N2 | OD1 | ASN- 38 | 3 | 166.43 | H-Bond (Ligand Donor) |
| C10 | CB | CYS- 45 | 4.35 | 0 | Hydrophobic |
| C10 | CD2 | TRP- 67 | 3.78 | 0 | Hydrophobic |
| C9 | CE2 | TRP- 67 | 3.75 | 0 | Hydrophobic |
| S1 | CZ2 | TRP- 67 | 3.69 | 0 | Hydrophobic |
| C10 | CB | CYS- 74 | 3.6 | 0 | Hydrophobic |
| O12 | OG | SER- 76 | 2.69 | 167.69 | H-Bond (Protein Donor) |
| S1 | CG2 | THR- 78 | 3.78 | 0 | Hydrophobic |
| S1 | CZ2 | TRP- 80 | 3.72 | 0 | Hydrophobic |
| C6 | CE2 | TRP- 97 | 3.36 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 115 | 2.77 | 170.33 | H-Bond (Ligand Donor) |
