sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 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 |
|---|---|
| A | 100 % |
| B-Factor: | 12.146 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.047 | 745.875 |
| % Hydrophobic | % Polar |
|---|---|
| 57.01 | 42.99 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 75.47 % |
| 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 |
|---|---|---|
| 36.4297 | 101.854 | 112.591 |
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 | 3.42 | 0 | Hydrophobic |
| SD | CZ | TYR- 21 | 3.93 | 0 | Hydrophobic |
| OXT | NE1 | TRP- 30 | 2.89 | 165.65 | H-Bond (Protein Donor) |
| CB | CZ2 | TRP- 30 | 3.75 | 0 | Hydrophobic |
| CE | CZ2 | TRP- 30 | 3.54 | 0 | Hydrophobic |
| O | NH2 | ARG- 40 | 2.61 | 128.09 | H-Bond (Protein Donor) |
| O | NH1 | ARG- 40 | 2.9 | 120.79 | H-Bond (Protein Donor) |
| O | CZ | ARG- 40 | 3.1 | 0 | Ionic (Protein Cationic) |
| N | O | ALA- 64 | 3.19 | 141.11 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 85 | 2.99 | 162.04 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 85 | 3.1 | 160.93 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 85 | 2.56 | 130.82 | H-Bond (Ligand Donor) |
| N3 | N | ALA- 86 | 3.36 | 141.76 | H-Bond (Protein Donor) |
| C2' | CB | SER- 87 | 4.49 | 0 | Hydrophobic |
| O2' | N | SER- 87 | 3.37 | 133.43 | H-Bond (Protein Donor) |
| N6 | OD1 | ASN- 116 | 2.81 | 156.22 | H-Bond (Ligand Donor) |
| C1' | CZ2 | TRP- 117 | 4.13 | 0 | Hydrophobic |
| N1 | N | TRP- 117 | 2.88 | 158.48 | H-Bond (Protein Donor) |
| N | O | LEU- 136 | 3.33 | 128.33 | H-Bond (Ligand Donor) |
| C5' | CB | SER- 139 | 3.5 | 0 | Hydrophobic |
