sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2005-12-05
| Name: | Aklanonic acid methyl ester cyclase AcmA |
|---|---|
| ID: | DNRD_STRGJ |
| AC: | O52646 |
| Organism: | Streptomyces galilaeus |
| Reign: | Bacteria |
| TaxID: | 33899 |
| EC Number: | 5.5.1.23 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 10 % |
| B | 90 % |
| B-Factor: | 25.845 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.082 | 1481.625 |
| % Hydrophobic | % Polar |
|---|---|
| 62.19 | 37.81 |
| According to VolSite | |
| HET Code: | NGV |
|---|---|
| Formula: | C21H12O7 |
| Molecular weight: | 376.316 g/mol |
| DrugBank ID: | DB04064 |
| Buried Surface Area: | 66.17 % |
| Polar Surface area: | 123.63 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 31.9379 | 35.8062 | 10.3275 |
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 |
| C3 | CG2 | THR- 36 | 3.49 | 0 | Hydrophobic |
| C1 | CE1 | PHE- 39 | 3.45 | 0 | Hydrophobic |
| DuAr | DuAr | TRP- 54 | 3.45 | 0 | Aromatic Face/Face |
| C18 | CH2 | TRP- 54 | 3.46 | 0 | Hydrophobic |
| C3 | CB | TRP- 54 | 4.09 | 0 | Hydrophobic |
| C15 | CE | MET- 91 | 3.73 | 0 | Hydrophobic |
| C11 | SD | MET- 91 | 3.49 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 92 | 3.58 | 0 | Hydrophobic |
| C15 | SD | MET- 94 | 3.3 | 0 | Hydrophobic |
| C15 | CH2 | TRP- 122 | 3.66 | 0 | Hydrophobic |
| C13 | CZ2 | TRP- 122 | 4.46 | 0 | Hydrophobic |
| C6 | CG | PRO- 123 | 4.42 | 0 | Hydrophobic |
| C7 | CB | PRO- 123 | 3.89 | 0 | Hydrophobic |
| C13 | CD2 | TYR- 125 | 3.97 | 0 | Hydrophobic |
| C8 | CG2 | THR- 128 | 3.68 | 0 | Hydrophobic |
| C13 | CB | TYR- 129 | 4.4 | 0 | Hydrophobic |
