sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
1995-07-07
| Name: | Non-fluorescent flavoprotein |
|---|---|
| ID: | LUXF_PHOPO |
| AC: | P12745 |
| Organism: | Photobacterium phosphoreum |
| Reign: | Bacteria |
| TaxID: | 659 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 53 % |
| B | 47 % |
| B-Factor: | 33.290 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.253 | 651.375 |
| % Hydrophobic | % Polar |
|---|---|
| 56.99 | 43.01 |
| According to VolSite | |
| HET Code: | FMA |
|---|---|
| Formula: | C31H44N4O11P |
| Molecular weight: | 679.675 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 50.03 % |
| Polar Surface area: | 257.17 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 20 |
| X | Y | Z |
|---|---|---|
| -4.58091 | 36.5923 | 101.767 |
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 |
| C14 | CG | PHE- 10 | 4.01 | 0 | Hydrophobic |
| C15 | CD1 | PHE- 10 | 4.34 | 0 | Hydrophobic |
| C4' | CE1 | TYR- 14 | 4.19 | 0 | Hydrophobic |
| C6' | CE1 | TYR- 14 | 3.95 | 0 | Hydrophobic |
| C7M | SD | MET- 25 | 4.15 | 0 | Hydrophobic |
| C13 | SD | MET- 25 | 3.88 | 0 | Hydrophobic |
| C5' | CB | MET- 25 | 3.43 | 0 | Hydrophobic |
| C12 | CB | ALA- 28 | 3.68 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 32 | 4.15 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 47 | 3.52 | 0 | Hydrophobic |
| C3B | CB | LYS- 61 | 3.91 | 0 | Hydrophobic |
| C5B | CD | LYS- 61 | 3.5 | 0 | Hydrophobic |
| C8 | CB | ALA- 63 | 3.73 | 0 | Hydrophobic |
| C7M | CZ | PHE- 65 | 4.06 | 0 | Hydrophobic |
| C8M | CE1 | PHE- 65 | 4.26 | 0 | Hydrophobic |
| C5' | CZ | PHE- 65 | 4.27 | 0 | Hydrophobic |
| C7' | CE2 | PHE- 65 | 4.25 | 0 | Hydrophobic |
| C14 | CD2 | PHE- 65 | 4.18 | 0 | Hydrophobic |
| C13 | CE2 | PHE- 65 | 3.43 | 0 | Hydrophobic |
| C15 | CG | LEU- 72 | 3.37 | 0 | Hydrophobic |
| C8M | CG2 | VAL- 74 | 4.07 | 0 | Hydrophobic |
| O1P | OG1 | THR- 81 | 2.98 | 156.22 | H-Bond (Protein Donor) |
| C7M | CG2 | ILE- 84 | 3.64 | 0 | Hydrophobic |
| C9A | CD1 | ILE- 84 | 3.81 | 0 | Hydrophobic |
| C1B | CD1 | ILE- 84 | 4.12 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 84 | 3.72 | 0 | Hydrophobic |
| C8 | CG2 | ILE- 84 | 3.3 | 0 | Hydrophobic |
| C7M | CE2 | TYR- 88 | 4.01 | 0 | Hydrophobic |
| O2' | OH | TYR- 88 | 2.75 | 166.37 | H-Bond (Protein Donor) |
| C7M | CD1 | LEU- 90 | 4.46 | 0 | Hydrophobic |
