sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.780 Å
X-ray
1994-02-17
| Name: | Streptavidin |
|---|---|
| ID: | SAV_STRAV |
| AC: | P22629 |
| Organism: | Streptomyces avidinii |
| Reign: | Bacteria |
| TaxID: | 1895 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 13.413 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.088 | 320.625 |
| % Hydrophobic | % Polar |
|---|---|
| 67.37 | 32.63 |
| According to VolSite | |
| HET Code: | HAB |
|---|---|
| Formula: | C13H9N2O3 |
| Molecular weight: | 241.222 g/mol |
| DrugBank ID: | DB07880 |
| Buried Surface Area: | 78.36 % |
| Polar Surface area: | 85.08 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 18.7294 | 4.91989 | 13.7501 |
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 |
| O | ND2 | ASN- 23 | 2.74 | 134.2 | H-Bond (Protein Donor) |
| C2 | CD1 | LEU- 25 | 4.35 | 0 | Hydrophobic |
| O | OG | SER- 27 | 2.57 | 143.76 | H-Bond (Protein Donor) |
| OXT | OG | SER- 27 | 2.94 | 142.05 | H-Bond (Protein Donor) |
| O | OH | TYR- 43 | 2.56 | 175.18 | H-Bond (Protein Donor) |
| C2' | CB | SER- 45 | 3.52 | 0 | Hydrophobic |
| C4' | CB | ASN- 49 | 4.39 | 0 | Hydrophobic |
| C2' | CB | ALA- 50 | 4.13 | 0 | Hydrophobic |
| C4' | CB | ALA- 50 | 3.35 | 0 | Hydrophobic |
| C5' | CB | TRP- 79 | 4.4 | 0 | Hydrophobic |
| C5' | CB | ALA- 86 | 4.43 | 0 | Hydrophobic |
| C5 | CG2 | THR- 90 | 4.03 | 0 | Hydrophobic |
| C5 | CE2 | TRP- 108 | 3.11 | 0 | Hydrophobic |
| C6' | CD1 | LEU- 110 | 4.1 | 0 | Hydrophobic |
