sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.360 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: | 19.447 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.728 | 283.500 |
| % Hydrophobic | % Polar |
|---|---|
| 64.29 | 35.71 |
| According to VolSite | |
| HET Code: | BTN |
|---|---|
| Formula: | C10H15N2O3S |
| Molecular weight: | 243.303 g/mol |
| DrugBank ID: | DB00121 |
| Buried Surface Area: | 75.09 % |
| 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 |
|---|---|---|
| 32.6914 | 12.5962 | -6.49175 |
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 |
| O3 | ND2 | ASN- 23 | 3.04 | 157.44 | H-Bond (Protein Donor) |
| O3 | OG | SER- 27 | 2.81 | 149.97 | H-Bond (Protein Donor) |
| O3 | OH | TYR- 43 | 2.71 | 170.66 | H-Bond (Protein Donor) |
| C7 | CB | SER- 45 | 3.98 | 0 | Hydrophobic |
| N2 | OG | SER- 45 | 2.88 | 172.95 | H-Bond (Ligand Donor) |
| C7 | CG2 | VAL- 47 | 4.42 | 0 | Hydrophobic |
| O12 | N | ASN- 49 | 3.03 | 169.47 | H-Bond (Protein Donor) |
| C9 | CB | ALA- 50 | 4.1 | 0 | Hydrophobic |
| C10 | CD2 | TRP- 79 | 3.53 | 0 | Hydrophobic |
| S1 | CZ2 | TRP- 79 | 3.69 | 0 | Hydrophobic |
| C8 | CE2 | TRP- 79 | 3.78 | 0 | Hydrophobic |
| C7 | CZ2 | TRP- 79 | 3.97 | 0 | Hydrophobic |
| C10 | CB | ALA- 86 | 4.29 | 0 | Hydrophobic |
| O11 | OG | SER- 88 | 2.89 | 172.72 | H-Bond (Protein Donor) |
| S1 | CG2 | THR- 90 | 3.65 | 0 | Hydrophobic |
| S1 | CZ2 | TRP- 92 | 3.79 | 0 | Hydrophobic |
| C6 | CE2 | TRP- 108 | 3.46 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 110 | 4.09 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 128 | 2.94 | 174.26 | H-Bond (Ligand Donor) |
