sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.950 Å
X-ray
2009-07-09
| Name: | AP4A hydrolase |
|---|---|
| ID: | O66548_AQUAE |
| AC: | O66548 |
| Organism: | Aquifex aeolicus |
| Reign: | Bacteria |
| TaxID: | 224324 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 42 % |
| B | 58 % |
| B-Factor: | 24.020 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.579 | 823.500 |
| % Hydrophobic | % Polar |
|---|---|
| 42.21 | 57.79 |
| According to VolSite | |
| HET Code: | B4P |
|---|---|
| Formula: | C20H24N10O19P4 |
| Molecular weight: | 832.355 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 34.71 % |
| Polar Surface area: | 484.53 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 27 |
| H-Bond Donors: | 6 |
| Rings: | 6 |
| Aromatic rings: | 4 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 14 |
| X | Y | Z |
|---|---|---|
| 21.7163 | 15.6746 | 30.3496 |
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 |
| O2B | NZ | LYS- 3 | 3.44 | 145.58 | H-Bond (Protein Donor) |
| O2G | NZ | LYS- 3 | 3.49 | 150.19 | H-Bond (Protein Donor) |
| O1D | NZ | LYS- 3 | 3.15 | 124.65 | H-Bond (Protein Donor) |
| O2D | NZ | LYS- 3 | 2.98 | 121.75 | H-Bond (Protein Donor) |
| O2E | N | LYS- 3 | 3.11 | 145.35 | H-Bond (Protein Donor) |
| N7B | N | LYS- 3 | 3.03 | 156.79 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 3 | 3.44 | 0 | Ionic (Protein Cationic) |
| O2G | NZ | LYS- 3 | 3.49 | 0 | Ionic (Protein Cationic) |
| O1D | NZ | LYS- 3 | 3.15 | 0 | Ionic (Protein Cationic) |
| O2D | NZ | LYS- 3 | 2.98 | 0 | Ionic (Protein Cationic) |
| C3E | CD | LYS- 3 | 4.17 | 0 | Hydrophobic |
| C2E | CG | LYS- 3 | 4.21 | 0 | Hydrophobic |
| N6B | O | LYS- 3 | 2.92 | 155.89 | H-Bond (Ligand Donor) |
| C4E | CZ | PHE- 5 | 3.47 | 0 | Hydrophobic |
| C1E | CE2 | PHE- 5 | 3.32 | 0 | Hydrophobic |
| C2F | CE1 | PHE- 5 | 3.52 | 0 | Hydrophobic |
| N1B | O | HOH- 282 | 2.82 | 179.97 | H-Bond (Protein Donor) |
