sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2002-04-30
| Name: | Ferredoxin-dependent glutamate synthase 2 |
|---|---|
| ID: | GLTS_SYNY3 |
| AC: | P55038 |
| Organism: | Synechocystis sp. |
| Reign: | Bacteria |
| TaxID: | 1111708 |
| EC Number: | 1.4.7.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 33.531 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 46 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.372 | 550.125 |
| % Hydrophobic | % Polar |
|---|---|
| 36.81 | 63.19 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 73.73 % |
| 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 |
|---|---|---|
| 182.693 | 223.939 | 33.2933 |
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 | SD | MET- 875 | 3.83 | 0 | Hydrophobic |
| C2' | CG | MET- 875 | 4.34 | 0 | Hydrophobic |
| C6 | CB | MET- 875 | 3.49 | 0 | Hydrophobic |
| C9A | CG | MET- 875 | 3.79 | 0 | Hydrophobic |
| N5 | N | SER- 876 | 3.24 | 144.39 | H-Bond (Protein Donor) |
| C6 | CB | ALA- 879 | 4.01 | 0 | Hydrophobic |
| C7M | CB | ALA- 879 | 4.43 | 0 | Hydrophobic |
| C7M | CD2 | LEU- 880 | 4 | 0 | Hydrophobic |
| O4 | N | GLU- 903 | 3.29 | 136.09 | H-Bond (Protein Donor) |
| O2 | NE2 | GLN- 944 | 3.17 | 166.88 | H-Bond (Protein Donor) |
| N3 | OE1 | GLN- 944 | 3.43 | 142.53 | H-Bond (Ligand Donor) |
| N1 | NZ | LYS- 1034 | 3.2 | 138.75 | H-Bond (Protein Donor) |
| O2 | NZ | LYS- 1034 | 2.71 | 157.57 | H-Bond (Protein Donor) |
| O3' | NZ | LYS- 1034 | 3.15 | 168.89 | H-Bond (Protein Donor) |
| O5' | N | GLY- 1064 | 3.24 | 148.31 | H-Bond (Protein Donor) |
| O2P | N | GLY- 1064 | 3.46 | 128.53 | H-Bond (Protein Donor) |
| O3' | OD2 | ASP- 1105 | 3.01 | 151.15 | H-Bond (Ligand Donor) |
| C5' | CB | ASP- 1105 | 4.27 | 0 | Hydrophobic |
| O1P | N | GLY- 1107 | 2.84 | 142.17 | H-Bond (Protein Donor) |
| O3P | N | GLY- 1128 | 2.89 | 156.69 | H-Bond (Protein Donor) |
| O2P | OG | SER- 1129 | 2.67 | 156.29 | H-Bond (Protein Donor) |
| O2P | N | SER- 1129 | 2.59 | 145.86 | H-Bond (Protein Donor) |
| O3P | N | SER- 1129 | 3.43 | 145.01 | H-Bond (Protein Donor) |
| C7M | SD | MET- 1132 | 3.92 | 0 | Hydrophobic |
| C8M | CE | MET- 1132 | 3.42 | 0 | Hydrophobic |
