sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2004-07-21
| Name: | 5-formyltetrahydrofolate cyclo-ligase |
|---|---|
| ID: | MTHFS_MYCPN |
| AC: | P75430 |
| Organism: | Mycoplasma pneumoniae |
| Reign: | Bacteria |
| TaxID: | 272634 |
| EC Number: | 6.3.3.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 17.888 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | ADP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.512 | 330.750 |
| % Hydrophobic | % Polar |
|---|---|
| 56.12 | 43.88 |
| According to VolSite | |
| HET Code: | THF |
|---|---|
| Formula: | C20H21N7O7 |
| Molecular weight: | 471.423 g/mol |
| DrugBank ID: | DB02800 |
| Buried Surface Area: | 36.95 % |
| Polar Surface area: | 224.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 13 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| 13.4252 | 19.7123 | 21.3401 |
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 |
| NA2 | OE2 | GLU- 55 | 2.7 | 152.72 | H-Bond (Ligand Donor) |
| N3 | OE1 | GLU- 55 | 2.69 | 138.92 | H-Bond (Ligand Donor) |
| N3 | OE2 | GLU- 55 | 3.27 | 128.8 | H-Bond (Ligand Donor) |
| C9 | CG2 | VAL- 78 | 3.72 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 78 | 3.93 | 0 | Hydrophobic |
| C4A | CG | PRO- 105 | 4.48 | 0 | Hydrophobic |
| C4A | CE1 | PHE- 118 | 4.13 | 0 | Hydrophobic |
| CP1 | CD1 | PHE- 118 | 4.23 | 0 | Hydrophobic |
| C13 | CB | PHE- 118 | 3.55 | 0 | Hydrophobic |
| C11 | CD | LYS- 120 | 3.6 | 0 | Hydrophobic |
| C14 | CG | LYS- 120 | 3.6 | 0 | Hydrophobic |
| C9 | CD1 | TYR- 122 | 3.71 | 0 | Hydrophobic |
| C6 | CE1 | TYR- 123 | 4.11 | 0 | Hydrophobic |
| CP1 | CE1 | TYR- 123 | 3.49 | 0 | Hydrophobic |
