sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
2002-12-02
| 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 |
|---|---|
| D | 100 % |
| B-Factor: | 31.377 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.557 | 519.750 |
| % Hydrophobic | % Polar |
|---|---|
| 41.56 | 58.44 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 72.55 % |
| 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 |
|---|---|---|
| 49.7626 | -10.3521 | 14.3588 |
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 |
| C3' | CE1 | TYR- 21 | 4.08 | 0 | Hydrophobic |
| OXT | NE1 | TRP- 30 | 3.31 | 154.79 | H-Bond (Protein Donor) |
| CB | CZ2 | TRP- 30 | 3.97 | 0 | Hydrophobic |
| CE | CZ2 | TRP- 30 | 3.52 | 0 | Hydrophobic |
| O | CZ | ARG- 40 | 3.06 | 0 | Ionic (Protein Cationic) |
| O3' | OD1 | ASP- 85 | 2.79 | 159.25 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 85 | 2.62 | 134.79 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 85 | 3.14 | 159.05 | H-Bond (Ligand Donor) |
| N3 | N | ALA- 86 | 3.45 | 140.5 | H-Bond (Protein Donor) |
| O2' | N | SER- 87 | 3.46 | 131.96 | H-Bond (Protein Donor) |
| SD | CE | MET- 90 | 4.2 | 0 | Hydrophobic |
| C3' | CE | MET- 90 | 4.35 | 0 | Hydrophobic |
| N6 | OD1 | ASN- 116 | 2.75 | 151.12 | H-Bond (Ligand Donor) |
| C1' | CZ2 | TRP- 117 | 4.03 | 0 | Hydrophobic |
| N1 | N | TRP- 117 | 2.78 | 154.24 | H-Bond (Protein Donor) |
| DuAr | DuAr | TRP- 117 | 3.65 | 0 | Aromatic Face/Face |
| CG | CB | SER- 139 | 4.28 | 0 | Hydrophobic |
| C5' | CB | SER- 139 | 3.34 | 0 | Hydrophobic |
