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
2003-04-12
| Name: | Guanidinoacetate N-methyltransferase |
|---|---|
| ID: | GAMT_RAT |
| AC: | P10868 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | 2.1.1.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 89 % |
| B | 11 % |
| B-Factor: | 9.287 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.118 | 1204.875 |
| % Hydrophobic | % Polar |
|---|---|
| 40.34 | 59.66 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 71.06 % |
| Polar Surface area: | 212.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -1.36296 | 8.06177 | 9.10219 |
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 |
| O3' | N | GLY- 69 | 2.82 | 134.32 | H-Bond (Protein Donor) |
| OXT | N | MET- 70 | 3.03 | 134.28 | H-Bond (Protein Donor) |
| OXT | N | ILE- 72 | 3.17 | 156.66 | H-Bond (Protein Donor) |
| O | N | ALA- 73 | 3 | 151.63 | H-Bond (Protein Donor) |
| O3' | OE2 | GLU- 89 | 2.91 | 146.72 | H-Bond (Ligand Donor) |
| O3' | OE1 | GLU- 89 | 3.38 | 154 | H-Bond (Ligand Donor) |
| O2' | OE1 | GLU- 89 | 2.59 | 161.02 | H-Bond (Ligand Donor) |
| N1 | N | TRP- 116 | 2.85 | 147.83 | H-Bond (Protein Donor) |
| N6 | OE2 | GLU- 117 | 3.02 | 148.73 | H-Bond (Ligand Donor) |
| N | OD2 | ASP- 134 | 3.2 | 159.43 | H-Bond (Ligand Donor) |
| N | OD2 | ASP- 134 | 3.2 | 0 | Ionic (Ligand Cationic) |
| CG | CE2 | TYR- 136 | 4.41 | 0 | Hydrophobic |
| SD | CZ | TYR- 136 | 3.3 | 0 | Hydrophobic |
| C5' | CE2 | TYR- 136 | 3.6 | 0 | Hydrophobic |
| SD | CB | ASP- 218 | 3.96 | 0 | Hydrophobic |
| CB | CB | ASP- 218 | 3.99 | 0 | Hydrophobic |
