sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2001-04-25
| Name: | Avidin |
|---|---|
| ID: | AVID_CHICK |
| AC: | P02701 |
| Organism: | Gallus gallus |
| Reign: | Eukaryota |
| TaxID: | 9031 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 25.573 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.717 | 259.875 |
| % Hydrophobic | % Polar |
|---|---|
| 61.04 | 38.96 |
| According to VolSite | |
| HET Code: | BNI |
|---|---|
| Formula: | C16H20N4O4S |
| Molecular weight: | 364.419 g/mol |
| DrugBank ID: | DB03549 |
| Buried Surface Area: | 44.72 % |
| Polar Surface area: | 141.35 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -1.68756 | 30.7675 | 27.1624 |
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 | OG | SER- 16 | 2.89 | 157.9 | H-Bond (Protein Donor) |
| O3 | OH | TYR- 33 | 2.65 | 156.79 | H-Bond (Protein Donor) |
| C10 | CD2 | TRP- 70 | 3.93 | 0 | Hydrophobic |
| C9 | CE2 | TRP- 70 | 4.32 | 0 | Hydrophobic |
| C8 | CZ2 | TRP- 70 | 3.5 | 0 | Hydrophobic |
| S1 | CZ2 | TRP- 70 | 3.42 | 0 | Hydrophobic |
| C8 | CZ | PHE- 72 | 4.36 | 0 | Hydrophobic |
| C10 | CE1 | PHE- 72 | 3.56 | 0 | Hydrophobic |
| O2 | OG | SER- 73 | 3.37 | 164.52 | H-Bond (Protein Donor) |
| O2 | OG | SER- 75 | 3.1 | 153.55 | H-Bond (Protein Donor) |
| S1 | CG2 | THR- 77 | 3.64 | 0 | Hydrophobic |
| C6 | CZ | PHE- 79 | 4.23 | 0 | Hydrophobic |
| C6 | CE2 | TRP- 97 | 3.44 | 0 | Hydrophobic |
| S1 | CD2 | LEU- 99 | 4.47 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 99 | 3.95 | 0 | Hydrophobic |
| N1 | OD1 | ASN- 118 | 3.07 | 172.67 | H-Bond (Ligand Donor) |
