sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2015-06-30
| Name: | O-acetyl-ADP-ribose deacetylase |
|---|---|
| ID: | YMDB_ECOLI |
| AC: | P0A8D6 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 47.684 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.039 | 556.875 |
| % Hydrophobic | % Polar |
|---|---|
| 56.36 | 43.64 |
| According to VolSite | |
| HET Code: | APR |
|---|---|
| Formula: | C15H21N5O14P2 |
| Molecular weight: | 557.300 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.23 % |
| Polar Surface area: | 316.8 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 18 |
| H-Bond Donors: | 6 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -17.4696 | -43.1476 | -6.86306 |
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 |
| N6 | OD1 | ASP- 11 | 2.67 | 166 | H-Bond (Ligand Donor) |
| N1 | N | ILE- 12 | 3.2 | 163.03 | H-Bond (Protein Donor) |
| C5' | CB | ALA- 23 | 4.46 | 0 | Hydrophobic |
| C3D | CB | ALA- 25 | 3.77 | 0 | Hydrophobic |
| O1D | N | GLY- 32 | 2.71 | 141.3 | H-Bond (Protein Donor) |
| O1D | N | GLY- 33 | 3.14 | 171.27 | H-Bond (Protein Donor) |
| C1' | CG2 | VAL- 34 | 4.22 | 0 | Hydrophobic |
| C5' | CG2 | VAL- 34 | 3.68 | 0 | Hydrophobic |
| O2A | N | VAL- 34 | 2.86 | 163.9 | H-Bond (Protein Donor) |
| C4' | CB | ALA- 120 | 4.43 | 0 | Hydrophobic |
| O1B | N | SER- 122 | 2.84 | 134.77 | H-Bond (Protein Donor) |
| O3' | OG1 | THR- 123 | 3 | 158.31 | H-Bond (Ligand Donor) |
| O2B | N | GLY- 124 | 2.76 | 128.84 | H-Bond (Protein Donor) |
| O1A | N | VAL- 125 | 3.37 | 166.71 | H-Bond (Protein Donor) |
| C1D | CG2 | VAL- 125 | 4.45 | 0 | Hydrophobic |
| C4D | CB | VAL- 125 | 3.97 | 0 | Hydrophobic |
| O2B | N | TYR- 126 | 3.05 | 162.54 | H-Bond (Protein Donor) |
| O5D | N | TYR- 126 | 3.5 | 128.32 | H-Bond (Protein Donor) |
| O3D | OH | TYR- 126 | 3.32 | 163.56 | H-Bond (Ligand Donor) |
| C4D | CE1 | TYR- 126 | 3.66 | 0 | Hydrophobic |
| C1' | CB | TYR- 159 | 3.89 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 159 | 3.93 | 0 | Aromatic Face/Face |
