sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2004-09-08
| Name: | Aclacinomycin 10-hydroxylase RdmB |
|---|---|
| ID: | RDMB_STREF |
| AC: | Q54527 |
| Organism: | Streptomyces purpurascens |
| Reign: | Bacteria |
| TaxID: | 1924 |
| EC Number: | 4.1.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 97 % |
| B | 3 % |
| B-Factor: | 37.953 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.534 | 1940.625 |
| % Hydrophobic | % Polar |
|---|---|
| 56.00 | 44.00 |
| According to VolSite | |
| HET Code: | DRA |
|---|---|
| Formula: | C40H50NO14 |
| Molecular weight: | 768.823 g/mol |
| DrugBank ID: | DB03219 |
| Buried Surface Area: | 55.08 % |
| Polar Surface area: | 217.83 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 4 |
| Rings: | 7 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 46.936 | 36.4292 | 113.586 |
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 |
| C10 | CH2 | TRP- 109 | 4.32 | 0 | Hydrophobic |
| C11 | CZ3 | TRP- 109 | 3.34 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 116 | 4.26 | 0 | Hydrophobic |
| C16 | SD | MET- 163 | 4.45 | 0 | Hydrophobic |
| C17 | SD | MET- 163 | 4.32 | 0 | Hydrophobic |
| C32 | CB | CYS- 165 | 4.44 | 0 | Hydrophobic |
| C36 | SD | MET- 196 | 3.52 | 0 | Hydrophobic |
| C2' | CE2 | PHE- 256 | 3.52 | 0 | Hydrophobic |
| O4 | ND2 | ASN- 260 | 3.03 | 150.16 | H-Bond (Protein Donor) |
| C36 | CD1 | LEU- 286 | 4.41 | 0 | Hydrophobic |
| C14 | CD2 | PHE- 300 | 3.78 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 304 | 4.39 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 304 | 3.59 | 0 | Hydrophobic |
| C15 | CE | MET- 308 | 3.56 | 0 | Hydrophobic |
| C3 | CE | MET- 312 | 3.45 | 0 | Hydrophobic |
| C40 | CB | SER- 339 | 3.57 | 0 | Hydrophobic |
| C6' | CB | SER- 341 | 4.21 | 0 | Hydrophobic |
| C32 | CB | SER- 341 | 4.48 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 344 | 3.94 | 0 | Hydrophobic |
| C6' | CD1 | LEU- 344 | 4.47 | 0 | Hydrophobic |
| C7 | CZ | PHE- 346 | 3.93 | 0 | Hydrophobic |
| C1' | CD2 | PHE- 346 | 3.85 | 0 | Hydrophobic |
| C8 | CD1 | PHE- 346 | 3.42 | 0 | Hydrophobic |
| C33 | CE2 | PHE- 348 | 4.01 | 0 | Hydrophobic |
| C34 | CZ | PHE- 348 | 4.15 | 0 | Hydrophobic |
| C38 | CZ | PHE- 348 | 3.52 | 0 | Hydrophobic |
