sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2002-06-14
| Name: | Glutathione synthetase |
|---|---|
| ID: | GSHB_YEAST |
| AC: | Q08220 |
| Organism: | Saccharomyces cerevisiae |
| Reign: | Eukaryota |
| TaxID: | 559292 |
| EC Number: | 6.3.2.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 19.197 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.330 | 918.000 |
| % Hydrophobic | % Polar |
|---|---|
| 39.71 | 60.29 |
| According to VolSite | |
| HET Code: | ANP |
|---|---|
| Formula: | C10H13N6O12P3 |
| Molecular weight: | 502.164 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.74 % |
| Polar Surface area: | 322.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -10.6892 | 1.013 | 3.70448 |
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' | CG1 | VAL- 145 | 4.01 | 0 | Hydrophobic |
| O1B | NZ | LYS- 324 | 2.72 | 0 | Ionic (Protein Cationic) |
| O2B | NZ | LYS- 324 | 3.7 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 324 | 3.15 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 324 | 3.15 | 166.98 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 382 | 2.65 | 150.42 | H-Bond (Protein Donor) |
| N7 | NZ | LYS- 382 | 3.02 | 153.64 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 382 | 2.65 | 0 | Ionic (Protein Cationic) |
| O2B | N | GLY- 387 | 3.27 | 164.15 | H-Bond (Protein Donor) |
| O5' | ND2 | ASN- 391 | 3.09 | 141.34 | H-Bond (Protein Donor) |
| C1' | CZ | TYR- 393 | 4.38 | 0 | Hydrophobic |
| N6 | O | GLU- 416 | 3.04 | 153.32 | H-Bond (Ligand Donor) |
| N1 | N | ILE- 418 | 2.81 | 167.84 | H-Bond (Protein Donor) |
| O3' | OE2 | GLU- 442 | 2.5 | 153.64 | H-Bond (Ligand Donor) |
| O2' | NZ | LYS- 469 | 2.95 | 147.94 | H-Bond (Protein Donor) |
| O2G | MG | MG- 502 | 2.23 | 0 | Metal Acceptor |
| O2A | MG | MG- 502 | 2.14 | 0 | Metal Acceptor |
| O1G | MG | MG- 503 | 2.19 | 0 | Metal Acceptor |
| O1B | MG | MG- 503 | 2.24 | 0 | Metal Acceptor |
| O2B | O | HOH- 2522 | 3.15 | 138.45 | H-Bond (Protein Donor) |
