sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2002-12-05
| 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 | 96 % |
| D | 4 % |
| B-Factor: | 33.126 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.715 | 303.750 |
| % Hydrophobic | % Polar |
|---|---|
| 54.44 | 45.56 |
| According to VolSite | |
| HET Code: | IMI |
|---|---|
| Formula: | C10H17N3O2S |
| Molecular weight: | 243.326 g/mol |
| DrugBank ID: | DB03353 |
| Buried Surface Area: | 75.97 % |
| 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 |
|---|---|---|
| 13.4228 | 6.94931 | 26.3889 |
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 | OG | SER- 27 | 3.08 | 138.26 | H-Bond (Ligand Donor) |
| C7 | CB | SER- 45 | 4.24 | 0 | Hydrophobic |
| N2 | OG | SER- 45 | 2.95 | 168.2 | H-Bond (Ligand Donor) |
| C4 | CG2 | VAL- 47 | 3.78 | 0 | Hydrophobic |
| O11 | N | ASN- 49 | 2.69 | 158.03 | H-Bond (Protein Donor) |
| C9 | CB | ALA- 50 | 3.98 | 0 | Hydrophobic |
| C8 | CE2 | TRP- 79 | 3.88 | 0 | Hydrophobic |
| C7 | CZ2 | TRP- 79 | 4.08 | 0 | Hydrophobic |
| S1 | CZ2 | TRP- 79 | 3.92 | 0 | Hydrophobic |
| C10 | CD2 | TRP- 79 | 3.68 | 0 | Hydrophobic |
| C10 | CB | ALA- 86 | 4.16 | 0 | Hydrophobic |
| O12 | OG | SER- 88 | 3.09 | 151.74 | H-Bond (Protein Donor) |
| S1 | CG2 | THR- 90 | 3.81 | 0 | Hydrophobic |
| S1 | CZ2 | TRP- 92 | 3.98 | 0 | Hydrophobic |
| C6 | CE2 | TRP- 108 | 3.45 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 110 | 4.09 | 0 | Hydrophobic |
| S1 | CD2 | LEU- 110 | 4.3 | 0 | Hydrophobic |
| C6 | CZ3 | TRP- 120 | 4.47 | 0 | Hydrophobic |
| C7 | CH2 | TRP- 120 | 4.12 | 0 | Hydrophobic |
| C2 | CZ3 | TRP- 120 | 3.47 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 128 | 3 | 166.82 | H-Bond (Protein Donor) |
