sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.620 Å
X-ray
1997-09-11
| Name: | Streptavidin |
|---|---|
| ID: | SAV_STRAV |
| AC: | P22629 |
| Organism: | Streptomyces avidinii |
| Reign: | Bacteria |
| TaxID: | 1895 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| D | 100 % |
| B-Factor: | 33.941 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.806 | 283.500 |
| % Hydrophobic | % Polar |
|---|---|
| 61.90 | 38.10 |
| According to VolSite | |
| HET Code: | IMI |
|---|---|
| Formula: | C10H17N3O2S |
| Molecular weight: | 243.326 g/mol |
| DrugBank ID: | DB03353 |
| Buried Surface Area: | 76.41 % |
| 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 |
|---|---|---|
| 19.1566 | 4.30238 | 13.3684 |
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 |
| C4 | CD1 | LEU- 25 | 4.33 | 0 | Hydrophobic |
| N3 | OG | SER- 27 | 2.77 | 148.65 | H-Bond (Ligand Donor) |
| C7 | CB | SER- 45 | 4.22 | 0 | Hydrophobic |
| N2 | OG | SER- 45 | 3.2 | 175.44 | H-Bond (Ligand Donor) |
| C4 | CG2 | VAL- 47 | 3.44 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 47 | 4.21 | 0 | Hydrophobic |
| O11 | N | ASN- 49 | 2.82 | 142 | H-Bond (Protein Donor) |
| C9 | CB | ALA- 50 | 3.93 | 0 | Hydrophobic |
| C8 | CE2 | TRP- 79 | 4.02 | 0 | Hydrophobic |
| S1 | CZ2 | TRP- 79 | 3.68 | 0 | Hydrophobic |
| C10 | CD2 | TRP- 79 | 3.76 | 0 | Hydrophobic |
| C7 | CZ2 | TRP- 79 | 3.9 | 0 | Hydrophobic |
| C10 | CB | ALA- 86 | 4.23 | 0 | Hydrophobic |
| O12 | OG | SER- 88 | 3.01 | 156.27 | H-Bond (Protein Donor) |
| S1 | CG2 | THR- 90 | 3.7 | 0 | Hydrophobic |
| S1 | CZ2 | TRP- 92 | 3.92 | 0 | Hydrophobic |
| C6 | CE2 | TRP- 108 | 3.45 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 110 | 3.93 | 0 | Hydrophobic |
| S1 | CD1 | LEU- 110 | 4.15 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 128 | 2.9 | 172.24 | H-Bond (Protein Donor) |
