sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.250 Å
X-ray
2011-01-07
| Name: | Acetylpolyamine amidohydrolase |
|---|---|
| ID: | APHA_MYCRA |
| AC: | Q48935 |
| Organism: | Mycoplana ramosa |
| Reign: | Bacteria |
| TaxID: | 40837 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 91 % |
| F | 9 % |
| B-Factor: | 25.149 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.758 | 806.625 |
| % Hydrophobic | % Polar |
|---|---|
| 42.26 | 57.74 |
| According to VolSite | |
| HET Code: | B3N |
|---|---|
| Formula: | C16H25N3O3 |
| Molecular weight: | 307.388 g/mol |
| DrugBank ID: | DB02565 |
| Buried Surface Area: | 59.3 % |
| Polar Surface area: | 81.67 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 27.3475 | 20.4946 | 68.5688 |
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 |
| C22 | CE1 | PHE- 27 | 3.82 | 0 | Hydrophobic |
| C16 | CE2 | PHE- 27 | 3.44 | 0 | Hydrophobic |
| C9 | CG | GLU- 117 | 3.82 | 0 | Hydrophobic |
| O4 | NE2 | HIS- 158 | 2.61 | 136.34 | H-Bond (Protein Donor) |
| N3 | NE2 | HIS- 159 | 2.85 | 127.57 | H-Bond (Ligand Donor) |
| C9 | CZ | TYR- 168 | 4.04 | 0 | Hydrophobic |
| C5 | CE2 | TYR- 168 | 3.48 | 0 | Hydrophobic |
| C9 | CD1 | PHE- 225 | 4.02 | 0 | Hydrophobic |
| C6 | CE2 | PHE- 225 | 4.13 | 0 | Hydrophobic |
| C8 | CD2 | PHE- 225 | 3.44 | 0 | Hydrophobic |
| C22 | CB | PRO- 290 | 4.49 | 0 | Hydrophobic |
| C21 | CB | PRO- 290 | 3.65 | 0 | Hydrophobic |
| C19 | CB | ILE- 291 | 4.04 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 291 | 3.57 | 0 | Hydrophobic |
| C22 | CE1 | TYR- 323 | 4.16 | 0 | Hydrophobic |
| O2 | ZN | ZN- 345 | 2.06 | 0 | Metal Acceptor |
| O4 | ZN | ZN- 345 | 1.92 | 0 | Metal Acceptor |
