sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.340 Å
X-ray
2012-10-19
| Name: | LOV protein |
|---|---|
| ID: | M1E1F8_RHOS5 |
| AC: | M1E1F8 |
| Organism: | Rhodobacter sphaeroides |
| Reign: | Bacteria |
| TaxID: | 349102 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 40.249 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.059 | 354.375 |
| % Hydrophobic | % Polar |
|---|---|
| 60.95 | 39.05 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 73.97 % |
| Polar Surface area: | 217.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 54.5976 | 0.404032 | -34.1821 |
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 |
| C8M | CB | VAL- 23 | 3.81 | 0 | Hydrophobic |
| C8 | CG2 | VAL- 23 | 3.61 | 0 | Hydrophobic |
| C9 | SG | CYS- 55 | 4.4 | 0 | Hydrophobic |
| C9A | CB | CYS- 55 | 3.65 | 0 | Hydrophobic |
| C6 | SG | CYS- 55 | 3.72 | 0 | Hydrophobic |
| C2' | CB | CYS- 55 | 4.15 | 0 | Hydrophobic |
| O1P | CZ | ARG- 56 | 3.97 | 0 | Ionic (Protein Cationic) |
| O2P | CZ | ARG- 56 | 3.93 | 0 | Ionic (Protein Cationic) |
| O2P | NH2 | ARG- 56 | 3.06 | 167.63 | H-Bond (Protein Donor) |
| C2' | CB | ARG- 56 | 4.14 | 0 | Hydrophobic |
| N1 | NE2 | GLN- 59 | 3.45 | 146.38 | H-Bond (Protein Donor) |
| O2 | NE2 | GLN- 59 | 3.13 | 139.78 | H-Bond (Protein Donor) |
| O4' | NE2 | GLN- 59 | 2.99 | 150.9 | H-Bond (Protein Donor) |
| O3P | NE | ARG- 68 | 2.73 | 144.23 | H-Bond (Protein Donor) |
| O3P | CZ | ARG- 68 | 3.86 | 0 | Ionic (Protein Cationic) |
| C5' | CG | ARG- 68 | 3.73 | 0 | Hydrophobic |
| C1' | CG2 | ILE- 71 | 4.46 | 0 | Hydrophobic |
| C4' | CG2 | ILE- 71 | 3.96 | 0 | Hydrophobic |
| C5' | CG | ARG- 72 | 3.94 | 0 | Hydrophobic |
| O3P | CZ | ARG- 72 | 3.74 | 0 | Ionic (Protein Cationic) |
| O3P | NH1 | ARG- 72 | 2.61 | 137.3 | H-Bond (Protein Donor) |
| C8M | CD2 | LEU- 75 | 3.8 | 0 | Hydrophobic |
| O2 | ND2 | ASN- 87 | 2.92 | 149.8 | H-Bond (Protein Donor) |
| N3 | OD1 | ASN- 87 | 2.87 | 151.48 | H-Bond (Ligand Donor) |
| C6 | CD1 | LEU- 99 | 4.38 | 0 | Hydrophobic |
| C9A | CD2 | LEU- 99 | 4.18 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 101 | 3.86 | 0 | Hydrophobic |
| C7M | CB | PHE- 114 | 3.85 | 0 | Hydrophobic |
| C8M | CB | PHE- 114 | 3.78 | 0 | Hydrophobic |
| O4 | NE2 | GLN- 118 | 2.67 | 152.59 | H-Bond (Protein Donor) |
| N5 | NE2 | GLN- 118 | 3.27 | 129.29 | H-Bond (Protein Donor) |
