sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
2011-07-30
| Name: | ATPase GET3 |
|---|---|
| ID: | GET3_YEAST |
| AC: | Q12154 |
| Organism: | Saccharomyces cerevisiae |
| Reign: | Eukaryota |
| TaxID: | 559292 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 94 % |
| D | 3 % |
| H | 3 % |
| B-Factor: | 91.261 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.042 | 833.625 |
| % Hydrophobic | % Polar |
|---|---|
| 43.32 | 56.68 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.26 % |
| Polar Surface area: | 260.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 38.3983 | 1.24167 | -18.7819 |
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 |
| O1B | N | GLY- 30 | 3.34 | 127.55 | H-Bond (Protein Donor) |
| O1B | N | THR- 32 | 2.9 | 150.87 | H-Bond (Protein Donor) |
| O3B | OG1 | THR- 32 | 3.2 | 150.29 | H-Bond (Protein Donor) |
| O2A | OG1 | THR- 32 | 3.29 | 136.15 | H-Bond (Protein Donor) |
| O1A | OG1 | THR- 33 | 3.4 | 163.71 | H-Bond (Protein Donor) |
| O1A | N | THR- 33 | 3.46 | 167.8 | H-Bond (Protein Donor) |
| N7 | ND2 | ASN- 272 | 2.85 | 155.41 | H-Bond (Protein Donor) |
| N6 | OD1 | ASN- 272 | 3.07 | 151.34 | H-Bond (Ligand Donor) |
| N6 | O | PRO- 315 | 3.11 | 165.72 | H-Bond (Ligand Donor) |
| N1 | N | CYS- 317 | 3.02 | 164.17 | H-Bond (Protein Donor) |
| C2' | CB | GLU- 320 | 4.27 | 0 | Hydrophobic |
| O3' | NH1 | ARG- 322 | 3.27 | 132.03 | H-Bond (Protein Donor) |
