sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2011-08-19
| Name: | Glycine N-methyltransferase |
|---|---|
| ID: | GNMT_RAT |
| AC: | P13255 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | 2.1.1.20 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 16 % |
| B | 37 % |
| C | 21 % |
| D | 26 % |
| B-Factor: | 18.584 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.068 | 783.000 |
| % Hydrophobic | % Polar |
|---|---|
| 53.45 | 46.55 |
| According to VolSite | |
| HET Code: | C2F |
|---|---|
| Formula: | C20H23N7O6 |
| Molecular weight: | 457.440 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.8 % |
| Polar Surface area: | 204.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 14.6432 | -20.4388 | 18.7661 |
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 |
| C11 | CB | SER- 3 | 3.8 | 0 | Hydrophobic |
| C7 | CD1 | TYR- 5 | 3.37 | 0 | Hydrophobic |
| C11 | CB | TYR- 5 | 3.76 | 0 | Hydrophobic |
| C15 | CB | TYR- 5 | 4.34 | 0 | Hydrophobic |
| C16 | CB | TYR- 5 | 4.08 | 0 | Hydrophobic |
| CB | CE1 | TYR- 5 | 3.29 | 0 | Hydrophobic |
| CG | CZ | TYR- 5 | 3.7 | 0 | Hydrophobic |
| C9 | CB | TYR- 5 | 3.69 | 0 | Hydrophobic |
| C17 | CB | TYR- 5 | 3.36 | 0 | Hydrophobic |
| C6 | CG2 | THR- 7 | 3.7 | 0 | Hydrophobic |
| C13 | CB | SER- 205 | 3.89 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 207 | 3.31 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 207 | 4.17 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 207 | 3.96 | 0 | Hydrophobic |
| OE1 | NE2 | HIS- 214 | 3.02 | 160.65 | H-Bond (Protein Donor) |
| C6 | SD | MET- 215 | 3.77 | 0 | Hydrophobic |
| C13 | CG2 | THR- 217 | 3.91 | 0 | Hydrophobic |
| C14 | CB | THR- 217 | 3.64 | 0 | Hydrophobic |
| O | NH2 | ARG- 239 | 2.81 | 172.64 | H-Bond (Protein Donor) |
