sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.350 Å
X-ray
2003-10-05
| Name: | Adenosine deaminase |
|---|---|
| ID: | ADA_BOVIN |
| AC: | P56658 |
| Organism: | Bos taurus |
| Reign: | Eukaryota |
| TaxID: | 9913 |
| EC Number: | 3.5.4.4 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 24.686 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.215 | 762.750 |
| % Hydrophobic | % Polar |
|---|---|
| 60.18 | 39.82 |
| According to VolSite | |
| HET Code: | FR9 |
|---|---|
| Formula: | C24H26N6O3 |
| Molecular weight: | 446.502 g/mol |
| DrugBank ID: | DB02830 |
| Buried Surface Area: | 61.41 % |
| Polar Surface area: | 127.2 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 49.7519 | 53.7767 | 19.078 |
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 |
| O15 | ND1 | HIS- 17 | 2.72 | 153.82 | H-Bond (Protein Donor) |
| DuAr | DuAr | HIS- 17 | 3.69 | 0 | Aromatic Face/Face |
| O15 | OD2 | ASP- 19 | 2.83 | 161.85 | H-Bond (Ligand Donor) |
| C32 | CD1 | LEU- 58 | 4.36 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 58 | 4.41 | 0 | Hydrophobic |
| C15 | CG | PHE- 61 | 3.3 | 0 | Hydrophobic |
| C15 | CB | PHE- 61 | 3.77 | 0 | Hydrophobic |
| C29 | CD2 | LEU- 62 | 3.44 | 0 | Hydrophobic |
| C13 | CZ | PHE- 65 | 4.48 | 0 | Hydrophobic |
| C19 | CE1 | PHE- 65 | 4.08 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 106 | 4.24 | 0 | Hydrophobic |
| C18 | CE | MET- 155 | 4.09 | 0 | Hydrophobic |
| C29 | CE | MET- 155 | 3.88 | 0 | Hydrophobic |
| C32 | CB | ASP- 185 | 3.36 | 0 | Hydrophobic |
| C10 | CB | THR- 269 | 3.82 | 0 | Hydrophobic |
| C7 | CG2 | THR- 269 | 3.42 | 0 | Hydrophobic |
| N10 | OD2 | ASP- 296 | 3.05 | 140.86 | H-Bond (Ligand Donor) |
| O9 | O | HOH- 1005 | 3.09 | 135.16 | H-Bond (Protein Donor) |
