sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.620 Å
X-ray
2012-07-13
| Name: | Luciferin 4-monooxygenase |
|---|---|
| ID: | LUCI_PHOPY |
| AC: | P08659 |
| Organism: | Photinus pyralis |
| Reign: | Eukaryota |
| TaxID: | 7054 |
| EC Number: | 1.13.12.7 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 25.508 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 43 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.166 | 1471.500 |
| % Hydrophobic | % Polar |
|---|---|
| 47.25 | 52.75 |
| According to VolSite | |
| HET Code: | SLU |
|---|---|
| Formula: | C21H17N8O8S3 |
| Molecular weight: | 605.603 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.22 % |
| Polar Surface area: | 304.71 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 4 |
| Rings: | 6 |
| Aromatic rings: | 5 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -32.1255 | 17.4712 | -16.6189 |
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 |
| O18 | NE2 | HIS- 245 | 3.01 | 145.32 | H-Bond (Protein Donor) |
| S9 | CD1 | PHE- 247 | 3.86 | 0 | Hydrophobic |
| C2 | CG2 | THR- 251 | 3.73 | 0 | Hydrophobic |
| N37 | N | GLY- 316 | 3 | 124.86 | H-Bond (Protein Donor) |
| N38 | OE1 | GLN- 338 | 2.7 | 151.82 | H-Bond (Ligand Donor) |
| N38 | O | GLY- 339 | 2.68 | 144.22 | H-Bond (Ligand Donor) |
| C24 | CE1 | TYR- 340 | 3.94 | 0 | Hydrophobic |
| C21 | CG | LEU- 342 | 4.35 | 0 | Hydrophobic |
| C23 | CG | LEU- 342 | 4.13 | 0 | Hydrophobic |
| O19 | N | THR- 343 | 3.34 | 170.57 | H-Bond (Protein Donor) |
| O19 | OG1 | THR- 343 | 3.15 | 168.17 | H-Bond (Protein Donor) |
| C2 | CB | ALA- 348 | 3.5 | 0 | Hydrophobic |
| O27 | OD2 | ASP- 422 | 2.79 | 150.31 | H-Bond (Ligand Donor) |
| O28 | OD2 | ASP- 422 | 3.16 | 127.19 | H-Bond (Ligand Donor) |
| O28 | OD1 | ASP- 422 | 2.67 | 165.13 | H-Bond (Ligand Donor) |
| O20 | NZ | LYS- 529 | 2.9 | 154.31 | H-Bond (Protein Donor) |
| C22 | CD | LYS- 529 | 3.89 | 0 | Hydrophobic |
| C25 | CD | LYS- 529 | 4.05 | 0 | Hydrophobic |
