sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.650 Å
X-ray
2012-03-26
| Name: | Reticuline oxidase |
|---|---|
| ID: | RETO_ESCCA |
| AC: | P30986 |
| Organism: | Eschscholzia californica |
| Reign: | Eukaryota |
| TaxID: | 3467 |
| EC Number: | 1.21.3.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 27.995 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.128 | 604.125 |
| % Hydrophobic | % Polar |
|---|---|
| 52.51 | 47.49 |
| According to VolSite | |
| HET Code: | REN |
|---|---|
| Formula: | C19H24NO4 |
| Molecular weight: | 330.398 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 71.08 % |
| Polar Surface area: | 63.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 28.1231 | 34.9739 | 21.4706 |
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 | CE1 | TYR- 106 | 4.33 | 0 | Hydrophobic |
| C23 | CE2 | TRP- 165 | 3.51 | 0 | Hydrophobic |
| C21 | CB | TRP- 165 | 4.1 | 0 | Hydrophobic |
| C23 | CB | SER- 280 | 3.57 | 0 | Hydrophobic |
| C25 | CD2 | LEU- 282 | 3.63 | 0 | Hydrophobic |
| C23 | CD1 | LEU- 295 | 3.61 | 0 | Hydrophobic |
| C7 | CE2 | PHE- 351 | 3.79 | 0 | Hydrophobic |
| C7 | CB | ASP- 352 | 3.64 | 0 | Hydrophobic |
| C5 | CB | ASP- 352 | 4.3 | 0 | Hydrophobic |
| O4 | OD1 | ASP- 352 | 2.76 | 159.36 | H-Bond (Ligand Donor) |
| C7 | CB | ARG- 354 | 4.48 | 0 | Hydrophobic |
| C8 | CB | PHE- 356 | 4.43 | 0 | Hydrophobic |
| C10 | CE1 | PHE- 356 | 3.91 | 0 | Hydrophobic |
| C7 | CD2 | PHE- 356 | 3.48 | 0 | Hydrophobic |
| C10 | CG2 | THR- 358 | 4.38 | 0 | Hydrophobic |
| C16 | CE1 | PHE- 386 | 4.17 | 0 | Hydrophobic |
| C18 | CB | ALA- 388 | 3.71 | 0 | Hydrophobic |
| O20 | ND2 | ASN- 390 | 2.91 | 135.39 | H-Bond (Protein Donor) |
| N12 | OE2 | GLU- 417 | 3.54 | 0 | Ionic (Ligand Cationic) |
| O20 | OE1 | GLU- 417 | 3.06 | 151.61 | H-Bond (Ligand Donor) |
| C8 | CG2 | ILE- 419 | 3.86 | 0 | Hydrophobic |
| C7 | CB | ALA- 421 | 3.93 | 0 | Hydrophobic |
| C1 | C7M | FAD- 601 | 4.48 | 0 | Hydrophobic |
