sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.990 Å
X-ray
2005-07-08
| 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: | 38.073 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.762 | 249.750 |
| % Hydrophobic | % Polar |
|---|---|
| 63.51 | 36.49 |
| According to VolSite | |
| HET Code: | GNG |
|---|---|
| Formula: | C10H13N5O4 |
| Molecular weight: | 267.241 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.99 % |
| Polar Surface area: | 134.99 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 11.4612 | 0.183895 | 4.13368 |
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' | CE2 | TRP- 70 | 3.88 | 0 | Hydrophobic |
| C1' | CE2 | TRP- 70 | 3.38 | 0 | Hydrophobic |
| C2' | CZ2 | TRP- 70 | 4.03 | 0 | Hydrophobic |
| C3' | CZ | PHE- 72 | 3.72 | 0 | Hydrophobic |
| C5' | CD2 | LEU- 99 | 4.49 | 0 | Hydrophobic |
| N1 | OD1 | ASN- 118 | 2.6 | 132.44 | H-Bond (Ligand Donor) |
