sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.480 Å
X-ray
1997-08-13
| 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: | 19.602 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.824 | 283.500 |
| % Hydrophobic | % Polar |
|---|---|
| 65.48 | 34.52 |
| According to VolSite | |
| HET Code: | IMI |
|---|---|
| Formula: | C10H17N3O2S |
| Molecular weight: | 243.326 g/mol |
| DrugBank ID: | DB03353 |
| Buried Surface Area: | 75.79 % |
| Polar Surface area: | 115.08 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 32.6556 | 12.6457 | -6.72269 |
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 |
| N3 | OD1 | ASN- 23 | 3.05 | 141.89 | H-Bond (Ligand Donor) |
| C4 | CD1 | LEU- 25 | 4.31 | 0 | Hydrophobic |
| N3 | OG | SER- 27 | 2.92 | 133.1 | H-Bond (Ligand Donor) |
| C7 | CB | SER- 45 | 4.08 | 0 | Hydrophobic |
| N2 | OG | SER- 45 | 3.03 | 176.47 | H-Bond (Ligand Donor) |
| C7 | CG2 | VAL- 47 | 4.37 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 47 | 3.61 | 0 | Hydrophobic |
| O12 | N | ASN- 49 | 2.98 | 169.72 | H-Bond (Protein Donor) |
| C9 | CB | ALA- 50 | 4.08 | 0 | Hydrophobic |
| C8 | CE2 | TRP- 79 | 3.96 | 0 | Hydrophobic |
| S1 | CZ2 | TRP- 79 | 3.62 | 0 | Hydrophobic |
| C10 | CD2 | TRP- 79 | 3.72 | 0 | Hydrophobic |
| C7 | CZ2 | TRP- 79 | 3.95 | 0 | Hydrophobic |
| C10 | CB | ALA- 86 | 4.3 | 0 | Hydrophobic |
| O11 | OG | SER- 88 | 2.79 | 172.61 | H-Bond (Protein Donor) |
| S1 | CG2 | THR- 90 | 3.81 | 0 | Hydrophobic |
| S1 | CZ2 | TRP- 92 | 3.99 | 0 | Hydrophobic |
| C6 | CE2 | TRP- 108 | 3.61 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 110 | 3.99 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 110 | 4.45 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 128 | 3.08 | 160.96 | H-Bond (Protein Donor) |
