sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.000 Å
X-ray
2012-07-31
| Name: | Streptavidin |
|---|---|
| ID: | SAV_STRAV |
| AC: | P22629 |
| Organism: | Streptomyces avidinii |
| Reign: | Bacteria |
| TaxID: | 1895 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 9.521 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.853 | 303.750 |
| % Hydrophobic | % Polar |
|---|---|
| 62.22 | 37.78 |
| According to VolSite | |
| HET Code: | BTN |
|---|---|
| Formula: | C10H15N2O3S |
| Molecular weight: | 243.303 g/mol |
| DrugBank ID: | DB00121 |
| Buried Surface Area: | 75.95 % |
| 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 |
|---|---|---|
| 29.8394 | 14.8257 | 12.3163 |
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 |
| C10 | CD2 | TRP- 79 | 3.61 | 0 | Hydrophobic |
| S1 | CZ2 | TRP- 79 | 3.69 | 0 | Hydrophobic |
| C9 | CE2 | TRP- 79 | 3.67 | 0 | Hydrophobic |
| C7 | CZ2 | TRP- 79 | 3.98 | 0 | Hydrophobic |
| C10 | CB | ALA- 86 | 4.1 | 0 | Hydrophobic |
| O12 | OG | SER- 88 | 2.8 | 171.11 | H-Bond (Protein Donor) |
| S1 | CG2 | THR- 90 | 3.75 | 0 | Hydrophobic |
| S1 | CZ2 | TRP- 92 | 3.74 | 0 | Hydrophobic |
| C6 | CE2 | TRP- 108 | 3.32 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 110 | 3.75 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 110 | 4.17 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 128 | 2.79 | 175.25 | H-Bond (Ligand Donor) |
| O3 | ND2 | ASN- 223 | 3 | 152.54 | H-Bond (Protein Donor) |
| O3 | OG | SER- 227 | 2.7 | 152.41 | H-Bond (Protein Donor) |
| O3 | OH | TYR- 243 | 2.72 | 169.8 | H-Bond (Protein Donor) |
| C7 | CB | SER- 245 | 4.12 | 0 | Hydrophobic |
| N2 | OG | SER- 245 | 2.96 | 168.26 | H-Bond (Ligand Donor) |
| C7 | CG2 | VAL- 247 | 4.31 | 0 | Hydrophobic |
| O11 | N | ASN- 249 | 2.88 | 164.5 | H-Bond (Protein Donor) |
