sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.400 Å
X-ray
2012-09-21
| Name: | FMN-binding protein |
|---|---|
| ID: | FMNB_DESVM |
| AC: | Q46604 |
| Organism: | Desulfovibrio vulgaris |
| Reign: | Bacteria |
| TaxID: | 883 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 63 % |
| B | 37 % |
| B-Factor: | 11.733 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.004 | 546.750 |
| % Hydrophobic | % Polar |
|---|---|
| 48.15 | 51.85 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 69.09 % |
| 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 |
|---|---|---|
| 5.29529 | 1.38194 | 5.53987 |
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 |
| C7M | CG2 | VAL- 15 | 3.83 | 0 | Hydrophobic |
| O1P | NE2 | HIS- 27 | 2.71 | 164.43 | H-Bond (Protein Donor) |
| O3P | NE2 | HIS- 27 | 3.45 | 127.18 | H-Bond (Protein Donor) |
| C2' | CB | VAL- 29 | 4.07 | 0 | Hydrophobic |
| C3' | CG1 | VAL- 29 | 3.92 | 0 | Hydrophobic |
| O2' | N | ASN- 30 | 2.84 | 154.71 | H-Bond (Protein Donor) |
| C8 | CB | ASN- 30 | 3.63 | 0 | Hydrophobic |
| O4 | OG1 | THR- 31 | 2.74 | 157.15 | H-Bond (Protein Donor) |
| C7M | CZ2 | TRP- 32 | 3.42 | 0 | Hydrophobic |
| N3 | O | PRO- 47 | 3 | 161.96 | H-Bond (Ligand Donor) |
| O2 | N | GLY- 49 | 2.79 | 149.26 | H-Bond (Protein Donor) |
| O2 | N | GLY- 50 | 2.96 | 148.23 | H-Bond (Protein Donor) |
| O4' | N | MET- 51 | 2.85 | 144.17 | H-Bond (Protein Donor) |
| O5' | N | MET- 51 | 3.08 | 123.51 | H-Bond (Protein Donor) |
| O2P | N | LYS- 53 | 2.96 | 170.04 | H-Bond (Protein Donor) |
| O3P | N | THR- 54 | 2.8 | 154.04 | H-Bond (Protein Donor) |
| O3P | OG1 | THR- 54 | 2.73 | 153.15 | H-Bond (Protein Donor) |
| C7 | CD2 | LEU- 122 | 3.74 | 0 | Hydrophobic |
| C8 | CB | LEU- 122 | 3.97 | 0 | Hydrophobic |
