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
2012-10-12
| Name: | LOV protein |
|---|---|
| ID: | M1E1G2_RHOS5 |
| AC: | M1E1G2 |
| Organism: | Rhodobacter sphaeroides |
| Reign: | Bacteria |
| TaxID: | 349102 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 57.740 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.308 | 388.125 |
| % Hydrophobic | % Polar |
|---|---|
| 51.30 | 48.70 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 75.98 % |
| 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 |
|---|---|---|
| -12.791 | -8.11645 | 15.3283 |
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 |
| C8 | CG2 | VAL- 23 | 3.91 | 0 | Hydrophobic |
| C8M | CB | VAL- 23 | 3.8 | 0 | Hydrophobic |
| C7M | CG2 | VAL- 23 | 3.53 | 0 | Hydrophobic |
| C6 | SG | CYS- 55 | 3.86 | 0 | Hydrophobic |
| C9A | CB | CYS- 55 | 3.67 | 0 | Hydrophobic |
| C2' | CB | CYS- 55 | 4.12 | 0 | Hydrophobic |
| C2' | CB | ARG- 56 | 3.96 | 0 | Hydrophobic |
| O4' | NE2 | GLN- 59 | 3.28 | 154.76 | H-Bond (Protein Donor) |
| O2P | NE | ARG- 68 | 3 | 160.83 | H-Bond (Protein Donor) |
| O3P | NE | ARG- 68 | 2.79 | 125.35 | H-Bond (Protein Donor) |
| O2P | CZ | ARG- 68 | 3.82 | 0 | Ionic (Protein Cationic) |
| O3P | CZ | ARG- 68 | 3.27 | 0 | Ionic (Protein Cationic) |
| C5' | CG | ARG- 68 | 3.83 | 0 | Hydrophobic |
| C1' | CG2 | ILE- 71 | 4.26 | 0 | Hydrophobic |
| C4' | CG2 | ILE- 71 | 3.83 | 0 | Hydrophobic |
| C5' | CG | ARG- 72 | 4.16 | 0 | Hydrophobic |
| O3P | NH1 | ARG- 72 | 2.65 | 148.51 | H-Bond (Protein Donor) |
| O3P | CZ | ARG- 72 | 3.76 | 0 | Ionic (Protein Cationic) |
| C8M | CD1 | LEU- 75 | 4.15 | 0 | Hydrophobic |
| O2 | ND2 | ASN- 87 | 2.85 | 147.12 | H-Bond (Protein Donor) |
| N3 | OD1 | ASN- 87 | 2.69 | 152.53 | H-Bond (Ligand Donor) |
| O4 | ND2 | ASN- 97 | 3.21 | 144.72 | H-Bond (Protein Donor) |
| C6 | CD1 | LEU- 99 | 4.44 | 0 | Hydrophobic |
| C9A | CD2 | LEU- 99 | 4.08 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 101 | 3.52 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 101 | 3.77 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 101 | 3.77 | 0 | Hydrophobic |
| C7M | CB | PHE- 114 | 3.95 | 0 | Hydrophobic |
| C8M | CB | PHE- 114 | 3.73 | 0 | Hydrophobic |
| O4 | NE2 | GLN- 118 | 2.79 | 154.06 | H-Bond (Protein Donor) |
| N5 | NE2 | GLN- 118 | 3.37 | 131.56 | H-Bond (Protein Donor) |
