sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2003-11-16
| Name: | mRNA cap guanine-N7 methyltransferase |
|---|---|
| ID: | MCES_ENCCU |
| AC: | Q8SR66 |
| Organism: | Encephalitozoon cuniculi |
| Reign: | Eukaryota |
| TaxID: | 284813 |
| EC Number: | 2.1.1.56 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 37.211 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.403 | 594.000 |
| % Hydrophobic | % Polar |
|---|---|
| 31.25 | 68.75 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 56.32 % |
| Polar Surface area: | 189.77 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 17.5349 | 27.6909 | 89.9741 |
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 |
| O | NZ | LYS- 54 | 2.83 | 151.13 | H-Bond (Protein Donor) |
| OXT | NZ | LYS- 54 | 3.07 | 142.25 | H-Bond (Protein Donor) |
| O | NZ | LYS- 54 | 2.83 | 0 | Ionic (Protein Cationic) |
| OXT | NZ | LYS- 54 | 3.07 | 0 | Ionic (Protein Cationic) |
| N | O | GLY- 72 | 3.12 | 168.07 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 94 | 2.88 | 169.66 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 94 | 3.28 | 147.8 | H-Bond (Ligand Donor) |
| C2' | CG2 | ILE- 95 | 4.35 | 0 | Hydrophobic |
| N6 | OD1 | ASP- 122 | 2.95 | 173.33 | H-Bond (Ligand Donor) |
| N1 | N | SER- 123 | 3.31 | 154.16 | H-Bond (Protein Donor) |
| N | O | GLN- 140 | 3.11 | 165.47 | H-Bond (Ligand Donor) |
| CE | CB | PHE- 141 | 3.7 | 0 | Hydrophobic |
| C1' | CB | SER- 142 | 4.23 | 0 | Hydrophobic |
| C5' | CB | SER- 142 | 3.72 | 0 | Hydrophobic |
| C5' | CE1 | TYR- 145 | 4.16 | 0 | Hydrophobic |
| OXT | O | HOH- 372 | 3.17 | 176.24 | H-Bond (Protein Donor) |
