sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2005-06-30
| Name: | Avidin |
|---|---|
| ID: | AVID_CHICK |
| AC: | P02701 |
| Organism: | Gallus gallus |
| Reign: | Eukaryota |
| TaxID: | 9031 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 36.180 |
|---|---|
| Number of residues: | 20 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.587 | 286.875 |
| % Hydrophobic | % Polar |
|---|---|
| 51.76 | 48.24 |
| According to VolSite | |
| HET Code: | 8DA |
|---|---|
| Formula: | C10H16N5O4 |
| Molecular weight: | 270.265 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.52 % |
| Polar Surface area: | 137.02 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 11.5486 | -0.593211 | 2.98053 |
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 |
| C2' | CD1 | LEU- 14 | 3.43 | 0 | Hydrophobic |
| O3' | OH | TYR- 33 | 3.15 | 132.33 | H-Bond (Protein Donor) |
| C1' | CH2 | TRP- 70 | 4.37 | 0 | Hydrophobic |
| C5' | CZ2 | TRP- 70 | 3.52 | 0 | Hydrophobic |
| C5' | CG2 | THR- 77 | 3.65 | 0 | Hydrophobic |
| C4' | CZ | PHE- 79 | 3.92 | 0 | Hydrophobic |
| O3' | OD1 | ASN- 118 | 2.85 | 153.81 | H-Bond (Ligand Donor) |
