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
2011-08-29
| 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 | 86 % |
| C | 5 % |
| D | 8 % |
| B-Factor: | 23.994 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.901 | 924.750 |
| % Hydrophobic | % Polar |
|---|---|
| 45.26 | 54.74 |
| According to VolSite | |
| HET Code: | NPK |
|---|---|
| Formula: | C20H22N3O9S |
| Molecular weight: | 480.468 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 67.27 % |
| Polar Surface area: | 188.35 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -17.1059 | 0.0512727 | -28.9816 |
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 |
| C39 | CB | ASP- 13 | 3.89 | 0 | Hydrophobic |
| C45 | CD1 | LEU- 14 | 4.47 | 0 | Hydrophobic |
| C38 | CB | LEU- 14 | 3.83 | 0 | Hydrophobic |
| O3 | OG | SER- 16 | 2.56 | 158.24 | H-Bond (Protein Donor) |
| O3 | OH | TYR- 33 | 2.85 | 176.35 | H-Bond (Protein Donor) |
| C2 | CB | THR- 35 | 4.43 | 0 | Hydrophobic |
| C8 | CG2 | THR- 35 | 3.82 | 0 | Hydrophobic |
| N2 | OG1 | THR- 35 | 2.69 | 174.55 | H-Bond (Ligand Donor) |
| O12 | OG1 | THR- 38 | 3.01 | 166.93 | H-Bond (Protein Donor) |
| O12 | N | ALA- 39 | 2.9 | 168.66 | H-Bond (Protein Donor) |
| S1 | CZ2 | TRP- 70 | 4.05 | 0 | Hydrophobic |
| C8 | CZ2 | TRP- 70 | 3.3 | 0 | Hydrophobic |
| C8 | CZ | PHE- 72 | 4.45 | 0 | Hydrophobic |
| O11 | OG | SER- 73 | 3.24 | 154.25 | H-Bond (Protein Donor) |
| S1 | CG2 | THR- 77 | 4.32 | 0 | Hydrophobic |
| S1 | CZ | PHE- 79 | 4.1 | 0 | Hydrophobic |
| C6 | CE2 | TRP- 97 | 3.55 | 0 | Hydrophobic |
| C34 | CZ2 | TRP- 97 | 4.33 | 0 | Hydrophobic |
| C2 | CZ3 | TRP- 110 | 4.29 | 0 | Hydrophobic |
| C6 | CE3 | TRP- 110 | 4.34 | 0 | Hydrophobic |
| C7 | CH2 | TRP- 110 | 3.8 | 0 | Hydrophobic |
| C36 | CB | TRP- 110 | 4.11 | 0 | Hydrophobic |
| C33 | CB | TRP- 110 | 3.65 | 0 | Hydrophobic |
| O55 | N | ILE- 119 | 3.34 | 171.39 | H-Bond (Protein Donor) |
