sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.590 Å
X-ray
2013-05-21
| Name: | S-adenosylmethionine synthase isoform type-2 |
|---|---|
| ID: | METK2_HUMAN |
| AC: | P31153 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.5.1.6 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 53 % |
| B | 47 % |
| B-Factor: | 59.065 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 43 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.376 | 435.375 |
| % Hydrophobic | % Polar |
|---|---|
| 51.94 | 48.06 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 74.25 % |
| 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 |
|---|---|---|
| -7.37856 | -6.88752 | -83.126 |
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 |
| OXT | NE2 | GLN- 113 | 3.22 | 150.17 | H-Bond (Protein Donor) |
| CE | CD1 | ILE- 117 | 4.03 | 0 | Hydrophobic |
| CG | CD1 | ILE- 117 | 3.53 | 0 | Hydrophobic |
| CE | CB | ASP- 134 | 4.02 | 0 | Hydrophobic |
| O2' | OD1 | ASP- 179 | 2.64 | 164.17 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 179 | 3.28 | 136.14 | H-Bond (Ligand Donor) |
| C4' | CD | LYS- 181 | 3.76 | 0 | Hydrophobic |
| C1' | CD | LYS- 181 | 3.79 | 0 | Hydrophobic |
| N1 | OG | SER- 247 | 2.91 | 141.19 | H-Bond (Protein Donor) |
| N6 | O | ARG- 249 | 3 | 140.31 | H-Bond (Ligand Donor) |
| C1' | CZ | PHE- 250 | 3.67 | 0 | Hydrophobic |
| C5' | CB | ASP- 258 | 4.31 | 0 | Hydrophobic |
| C3' | CB | ASP- 258 | 3.89 | 0 | Hydrophobic |
| CG | CB | ASP- 258 | 3.92 | 0 | Hydrophobic |
| O3' | OD2 | ASP- 258 | 3.13 | 158.35 | H-Bond (Ligand Donor) |
| CE | CD1 | ILE- 322 | 3.87 | 0 | Hydrophobic |
