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
2009-04-28
| Name: | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase |
|---|---|
| ID: | TYW2_METJA |
| AC: | Q58952 |
| Organism: | Methanocaldococcus jannaschii |
| Reign: | Archaea |
| TaxID: | 243232 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 50.232 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.772 | 634.500 |
| % Hydrophobic | % Polar |
|---|---|
| 53.72 | 46.28 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 67.6 % |
| 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 |
|---|---|---|
| -11.7799 | -14.0229 | -22.5688 |
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 |
| CG | CE | MET- 78 | 4.2 | 0 | Hydrophobic |
| C1' | CB | PHE- 104 | 4.46 | 0 | Hydrophobic |
| C4' | CB | PHE- 104 | 4.27 | 0 | Hydrophobic |
| CB | CD1 | TYR- 109 | 4.23 | 0 | Hydrophobic |
| CE | CE1 | TYR- 109 | 3.74 | 0 | Hydrophobic |
| O3' | OE2 | GLU- 127 | 3.4 | 135.94 | H-Bond (Ligand Donor) |
| O3' | OE1 | GLU- 127 | 3.08 | 169.67 | H-Bond (Ligand Donor) |
| O2' | OE2 | GLU- 127 | 2.66 | 159.25 | H-Bond (Ligand Donor) |
| N3 | N | LYS- 128 | 3.31 | 132.15 | H-Bond (Protein Donor) |
| N6 | OD1 | ASP- 154 | 3.25 | 156.52 | H-Bond (Ligand Donor) |
| N1 | N | ASN- 155 | 2.98 | 169.76 | H-Bond (Protein Donor) |
| C5' | CD1 | TYR- 171 | 4.27 | 0 | Hydrophobic |
