sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.520 Å
X-ray
2007-08-20
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.700 | 8.890 | 8.940 | 0.140 | 9.090 | 6 |
| 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: | 30.912 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.093 | 884.250 |
| % Hydrophobic | % Polar |
|---|---|
| 58.78 | 41.22 |
| According to VolSite | |
| HET Code: | EH9 |
|---|---|
| Formula: | C14H23N5O |
| Molecular weight: | 277.365 g/mol |
| DrugBank ID: | DB07711 |
| Buried Surface Area: | 60.94 % |
| Polar Surface area: | 89.85 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 10.7586 | 15.6032 | 20.9703 |
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 |
| O38 | ND1 | HIS- 14 | 2.51 | 151.78 | H-Bond (Protein Donor) |
| O38 | OD2 | ASP- 16 | 2.98 | 150.18 | H-Bond (Ligand Donor) |
| O38 | OD1 | ASP- 16 | 3.37 | 124.44 | H-Bond (Ligand Donor) |
| C34 | CE2 | PHE- 58 | 4.29 | 0 | Hydrophobic |
| C34 | CB | LEU- 59 | 4.13 | 0 | Hydrophobic |
| C28 | CG | PHE- 62 | 4.3 | 0 | Hydrophobic |
| C21 | CE2 | PHE- 62 | 3.59 | 0 | Hydrophobic |
| C40 | CB | SER- 100 | 4.4 | 0 | Hydrophobic |
| C28 | CD1 | LEU- 103 | 3.87 | 0 | Hydrophobic |
| C26 | CD1 | LEU- 103 | 3.94 | 0 | Hydrophobic |
| C28 | CH2 | TRP- 114 | 3.95 | 0 | Hydrophobic |
| C40 | CB | CYS- 150 | 4.28 | 0 | Hydrophobic |
| C26 | CE | MET- 152 | 4.25 | 0 | Hydrophobic |
| C30 | CE | MET- 152 | 4.13 | 0 | Hydrophobic |
| C40 | SD | MET- 152 | 3.67 | 0 | Hydrophobic |
| C40 | CB | ALA- 180 | 3.94 | 0 | Hydrophobic |
