sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.640 Å
X-ray
2012-10-12
| Name: | LOV protein |
|---|---|
| ID: | M1E1F9_RHOS5 |
| AC: | M1E1F9 |
| Organism: | Rhodobacter sphaeroides |
| Reign: | Bacteria |
| TaxID: | 349102 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 22.399 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.615 | 384.750 |
| % Hydrophobic | % Polar |
|---|---|
| 56.14 | 43.86 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 75.63 % |
| 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 |
|---|---|---|
| -41.9109 | 27.6581 | 22.0058 |
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 | 3.69 | 0 | Hydrophobic |
| C7M | CG2 | VAL- 23 | 3.43 | 0 | Hydrophobic |
| O2' | OD1 | ASN- 54 | 2.73 | 168.53 | H-Bond (Ligand Donor) |
| C6 | SG | CYS- 55 | 3.83 | 0 | Hydrophobic |
| C9A | CB | CYS- 55 | 3.57 | 0 | Hydrophobic |
| C2' | CB | CYS- 55 | 4.14 | 0 | Hydrophobic |
| O1P | NH2 | ARG- 56 | 3.46 | 130.53 | H-Bond (Protein Donor) |
| O1P | NE | ARG- 56 | 2.77 | 173.71 | H-Bond (Protein Donor) |
| O3P | NH2 | ARG- 56 | 2.6 | 152.85 | H-Bond (Protein Donor) |
| O1P | CZ | ARG- 56 | 3.56 | 0 | Ionic (Protein Cationic) |
| O3P | CZ | ARG- 56 | 3.5 | 0 | Ionic (Protein Cationic) |
| C2' | CB | ARG- 56 | 4.14 | 0 | Hydrophobic |
| O2 | NE2 | GLN- 59 | 2.88 | 157.97 | H-Bond (Protein Donor) |
| O4' | NE2 | GLN- 59 | 2.8 | 142.18 | H-Bond (Protein Donor) |
| C4' | CG | ARG- 68 | 4.45 | 0 | Hydrophobic |
| C5' | CB | ARG- 68 | 4 | 0 | Hydrophobic |
| O2P | NE | ARG- 68 | 3.15 | 136.66 | H-Bond (Protein Donor) |
| O2P | NH2 | ARG- 68 | 3.16 | 136.07 | H-Bond (Protein Donor) |
| O2P | CZ | ARG- 68 | 3.56 | 0 | Ionic (Protein Cationic) |
| C1' | CG2 | ILE- 71 | 4.18 | 0 | Hydrophobic |
| C5' | CG2 | ILE- 71 | 3.9 | 0 | Hydrophobic |
| O2P | NE | ARG- 72 | 3.04 | 166.92 | H-Bond (Protein Donor) |
| O2P | CZ | ARG- 72 | 3.78 | 0 | Ionic (Protein Cationic) |
| C8M | CD2 | LEU- 75 | 3.77 | 0 | Hydrophobic |
| O2 | ND2 | ASN- 87 | 2.9 | 152.02 | H-Bond (Protein Donor) |
| N3 | OD1 | ASN- 87 | 2.89 | 167.63 | H-Bond (Ligand Donor) |
| O4 | ND2 | ASN- 97 | 3.28 | 131.46 | H-Bond (Protein Donor) |
| C9A | CD1 | LEU- 99 | 4.41 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 101 | 3.67 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 101 | 3.89 | 0 | Hydrophobic |
| C7M | CB | PHE- 114 | 4.03 | 0 | Hydrophobic |
| C8M | CB | PHE- 114 | 3.73 | 0 | Hydrophobic |
| O4 | NE2 | GLN- 118 | 2.9 | 153.05 | H-Bond (Protein Donor) |
| N5 | NE2 | GLN- 118 | 3.29 | 129.66 | H-Bond (Protein Donor) |
