sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2007-07-03
| Name: | ATP synthase subunit alpha, mitochondrial | ATP synthase subunit beta, mitochondrial |
|---|---|---|
| ID: | ATPA_BOVIN | ATPB_BOVIN |
| AC: | P19483 | P00829 |
| Organism: | Bos taurus | |
| Reign: | Eukaryota | |
| TaxID: | 9913 | |
| EC Number: | / | 3.6.3.14 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 26 % |
| D | 74 % |
| B-Factor: | 26.910 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.198 | 891.000 |
| % Hydrophobic | % Polar |
|---|---|
| 56.06 | 43.94 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.22 % |
| 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 |
|---|---|---|
| -35.1895 | 41.7554 | 0.707148 |
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 |
| O3B | N | GLY- 159 | 2.8 | 146.79 | H-Bond (Protein Donor) |
| O1B | N | VAL- 160 | 3.35 | 127.17 | H-Bond (Protein Donor) |
| O1B | N | GLY- 161 | 2.94 | 154.66 | H-Bond (Protein Donor) |
| O3A | N | GLY- 161 | 3.26 | 128.28 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 162 | 2.89 | 149.06 | H-Bond (Protein Donor) |
| O1B | N | LYS- 162 | 2.77 | 163.41 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 162 | 2.89 | 0 | Ionic (Protein Cationic) |
| O3B | NZ | LYS- 162 | 3.53 | 0 | Ionic (Protein Cationic) |
| O2B | N | THR- 163 | 3.1 | 154.97 | H-Bond (Protein Donor) |
| O2A | N | VAL- 164 | 2.95 | 174.51 | H-Bond (Protein Donor) |
| C3' | CG2 | VAL- 164 | 4.11 | 0 | Hydrophobic |
| C1' | CZ | TYR- 345 | 3.82 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 345 | 3.64 | 0 | Aromatic Face/Face |
| C4' | CG1 | VAL- 371 | 4.48 | 0 | Hydrophobic |
| O2' | O | SER- 372 | 3.21 | 127.27 | H-Bond (Ligand Donor) |
| O3B | CZ | ARG- 373 | 3.74 | 0 | Ionic (Protein Cationic) |
| O1A | CZ | ARG- 373 | 3.96 | 0 | Ionic (Protein Cationic) |
| O3B | NH1 | ARG- 373 | 2.86 | 176.07 | H-Bond (Protein Donor) |
| O1A | NH1 | ARG- 373 | 2.81 | 136.05 | H-Bond (Protein Donor) |
| C4' | CG | ARG- 373 | 4.25 | 0 | Hydrophobic |
| C3' | CZ | PHE- 424 | 4.11 | 0 | Hydrophobic |
| C2' | CG | PHE- 424 | 3.68 | 0 | Hydrophobic |
| O2B | MG | MG- 1477 | 2.24 | 0 | Metal Acceptor |
