sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.450 Å
X-ray
2003-07-17
| 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: | 11.915 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 5 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.355 | 1080.000 |
| % Hydrophobic | % Polar |
|---|---|
| 55.63 | 44.38 |
| According to VolSite | |
| HET Code: | AKT |
|---|---|
| Formula: | C28H32NO8 |
| Molecular weight: | 510.556 g/mol |
| DrugBank ID: | DB04131 |
| Buried Surface Area: | 64.43 % |
| Polar Surface area: | 143.62 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 11.6372 | 13.8845 | 10.1763 |
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 | 4.4 | 0 | Hydrophobic |
| C2' | SD | MET- 103 | 4.23 | 0 | Hydrophobic |
| C6 | CB | MET- 103 | 3.63 | 0 | Hydrophobic |
| C2 | CG2 | ILE- 132 | 4.18 | 0 | Hydrophobic |
| C3 | CB | ILE- 132 | 3.99 | 0 | Hydrophobic |
| C5' | CE2 | PHE- 134 | 4.48 | 0 | Hydrophobic |
| C17 | CE2 | PHE- 134 | 3.27 | 0 | Hydrophobic |
| C4 | CB | PHE- 134 | 3.4 | 0 | Hydrophobic |
| C16 | CG | PHE- 134 | 3.43 | 0 | Hydrophobic |
| N3' | OD2 | ASP- 135 | 3.21 | 133.32 | H-Bond (Ligand Donor) |
| N3' | OD1 | ASP- 135 | 3 | 145.76 | H-Bond (Ligand Donor) |
| N3' | OD2 | ASP- 135 | 3.21 | 0 | Ionic (Ligand Cationic) |
| N3' | OD1 | ASP- 135 | 3 | 0 | Ionic (Ligand Cationic) |
| C6' | CD1 | ILE- 138 | 3.92 | 0 | Hydrophobic |
| C14 | CE1 | PHE- 158 | 3.44 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 162 | 3.96 | 0 | Hydrophobic |
| C14 | CE | MET- 165 | 4.45 | 0 | Hydrophobic |
| C1' | CD1 | TYR- 220 | 3.99 | 0 | Hydrophobic |
| C5' | CD1 | TYR- 220 | 4.13 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 250 | 3.66 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 250 | 4 | 0 | Hydrophobic |
| C1 | CB | ALA- 251 | 4.23 | 0 | Hydrophobic |
