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
2003-07-18
| Name: | Aclacinomycin methylesterase RdmC |
|---|---|
| ID: | RDMC_STREF |
| AC: | Q54528 |
| Organism: | Streptomyces purpurascens |
| Reign: | Bacteria |
| TaxID: | 1924 |
| EC Number: | 3.1.1.95 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 17.907 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.356 | 1147.500 |
| % Hydrophobic | % Polar |
|---|---|
| 54.12 | 45.88 |
| According to VolSite | |
| HET Code: | AKA |
|---|---|
| Formula: | C40H50NO13 |
| Molecular weight: | 752.824 g/mol |
| DrugBank ID: | DB01806 |
| Buried Surface Area: | 48.75 % |
| Polar Surface area: | 197.6 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 13 |
| H-Bond Donors: | 3 |
| Rings: | 7 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 14.2145 | 12.043 | 11.0368 |
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 |
| C11 | CB | SER- 102 | 4.37 | 0 | Hydrophobic |
| C2' | SD | MET- 103 | 4.36 | 0 | Hydrophobic |
| C20 | CB | MET- 103 | 3.8 | 0 | Hydrophobic |
| C6 | CB | MET- 103 | 3.59 | 0 | Hydrophobic |
| C2 | CG2 | ILE- 132 | 4 | 0 | Hydrophobic |
| C3 | CB | ILE- 132 | 4.03 | 0 | Hydrophobic |
| C5' | CE2 | PHE- 134 | 4.41 | 0 | Hydrophobic |
| C17 | CE2 | PHE- 134 | 3.28 | 0 | Hydrophobic |
| C4 | CB | PHE- 134 | 3.42 | 0 | Hydrophobic |
| C16 | CG | PHE- 134 | 3.45 | 0 | Hydrophobic |
| N3' | OD2 | ASP- 135 | 3.4 | 131.6 | H-Bond (Ligand Donor) |
| N3' | OD1 | ASP- 135 | 3.09 | 154.17 | H-Bond (Ligand Donor) |
| N3' | OD2 | ASP- 135 | 3.4 | 0 | Ionic (Ligand Cationic) |
| N3' | OD1 | ASP- 135 | 3.09 | 0 | Ionic (Ligand Cationic) |
| C32 | CB | ASP- 135 | 3.84 | 0 | Hydrophobic |
| C6' | CD1 | ILE- 138 | 3.88 | 0 | Hydrophobic |
| C6' | CZ | PHE- 158 | 4.16 | 0 | Hydrophobic |
| C13 | CE1 | PHE- 158 | 3.63 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 162 | 4.06 | 0 | Hydrophobic |
| C14 | CE | MET- 165 | 4.41 | 0 | Hydrophobic |
| C36 | CB | TYR- 220 | 4.44 | 0 | Hydrophobic |
| C5' | CD1 | TYR- 220 | 4.26 | 0 | Hydrophobic |
| C1' | CD1 | TYR- 220 | 3.94 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 250 | 3.7 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 250 | 3.93 | 0 | Hydrophobic |
