sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.410 Å
X-ray
2008-09-29
| Name: | mRNA cap guanine-N7 methyltransferase |
|---|---|
| ID: | MCES_HUMAN |
| AC: | O43148 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.1.1.56 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 28.858 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.443 | 300.375 |
| % Hydrophobic | % Polar |
|---|---|
| 57.30 | 42.70 |
| According to VolSite | |
| HET Code: | SFG |
|---|---|
| Formula: | C15H24N7O5 |
| Molecular weight: | 382.395 g/mol |
| DrugBank ID: | DB01910 |
| Buried Surface Area: | 55.87 % |
| Polar Surface area: | 214.71 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 1.48667 | -7.91219 | 31.9048 |
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- 17 | 2.78 | 167.14 | H-Bond (Protein Donor) |
| OXT | NZ | LYS- 17 | 3.27 | 129.82 | H-Bond (Protein Donor) |
| O | NZ | LYS- 17 | 2.78 | 0 | Ionic (Protein Cationic) |
| OXT | NZ | LYS- 17 | 3.27 | 0 | Ionic (Protein Cationic) |
| N | O | GLY- 42 | 2.78 | 150.77 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 64 | 3.43 | 123.49 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 64 | 2.76 | 146.72 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 64 | 2.85 | 152 | H-Bond (Ligand Donor) |
| N3 | N | ILE- 65 | 3.31 | 133.82 | H-Bond (Protein Donor) |
| C1' | CG2 | ILE- 65 | 4.29 | 0 | Hydrophobic |
| N6 | OD1 | ASP- 98 | 2.81 | 127.56 | H-Bond (Ligand Donor) |
| N1 | N | SER- 99 | 3.26 | 146.14 | H-Bond (Protein Donor) |
| N | O | GLN- 121 | 3.02 | 162.83 | H-Bond (Ligand Donor) |
| CB | CB | PHE- 122 | 4.16 | 0 | Hydrophobic |
| C1' | CG1 | VAL- 123 | 4.46 | 0 | Hydrophobic |
| C4' | CG2 | VAL- 123 | 3.78 | 0 | Hydrophobic |
| C5' | CE1 | TYR- 126 | 3.79 | 0 | Hydrophobic |
