sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 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 | 94 % |
| B | 6 % |
| B-Factor: | 25.889 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.112 | 772.875 |
| % Hydrophobic | % Polar |
|---|---|
| 55.46 | 44.54 |
| According to VolSite | |
| HET Code: | AKV |
|---|---|
| Formula: | C22H20O8 |
| Molecular weight: | 412.389 g/mol |
| DrugBank ID: | DB04624 |
| Buried Surface Area: | 63.43 % |
| Polar Surface area: | 147.01 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 32.6534 | 35.2077 | 9.17543 |
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 |
| C7 | CE1 | PHE- 39 | 4.33 | 0 | Hydrophobic |
| C8 | CZ | PHE- 39 | 3.61 | 0 | Hydrophobic |
| O23 | ND2 | ASN- 51 | 2.82 | 132.49 | H-Bond (Protein Donor) |
| C10 | CZ3 | TRP- 54 | 4.21 | 0 | Hydrophobic |
| C8 | CD2 | TRP- 54 | 3.25 | 0 | Hydrophobic |
| C20 | CZ3 | TRP- 54 | 3.41 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 55 | 4.04 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 55 | 3.66 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 83 | 3.93 | 0 | Hydrophobic |
| C3 | CE | MET- 91 | 3.64 | 0 | Hydrophobic |
| C16 | SD | MET- 91 | 3.7 | 0 | Hydrophobic |
| O16 | NE2 | GLN- 105 | 3.02 | 153.65 | H-Bond (Protein Donor) |
| C11 | CG | PRO- 123 | 3.9 | 0 | Hydrophobic |
| C2 | CB | TYR- 125 | 4.27 | 0 | Hydrophobic |
| C1 | CG2 | THR- 128 | 3.67 | 0 | Hydrophobic |
