sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2011-08-03
| Name: | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase |
|---|---|
| ID: | NADA_APLCA |
| AC: | P29241 |
| Organism: | Aplysia californica |
| Reign: | Eukaryota |
| TaxID: | 6500 |
| EC Number: | 3.2.2.6 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 100 % |
| B-Factor: | 49.655 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.148 | 317.250 |
| % Hydrophobic | % Polar |
|---|---|
| 50.00 | 50.00 |
| According to VolSite | |
| HET Code: | AV1 |
|---|---|
| Formula: | C15H20BrN5O13P2 |
| Molecular weight: | 620.197 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 44.05 % |
| Polar Surface area: | 296.57 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 5 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -36.5684 | -34.1831 | -1.72136 |
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 |
| C1D | CZ2 | TRP- 77 | 3.81 | 0 | Hydrophobic |
| C5D | CZ3 | TRP- 77 | 3.7 | 0 | Hydrophobic |
| C3D | CE2 | TRP- 77 | 3.48 | 0 | Hydrophobic |
| O3D | N | TRP- 77 | 3 | 159.18 | H-Bond (Protein Donor) |
| O2N | OG | SER- 78 | 3.36 | 158.97 | H-Bond (Protein Donor) |
| O1A | N | GLY- 79 | 2.68 | 146.49 | H-Bond (Protein Donor) |
| BR1 | CB | TYR- 81 | 4 | 0 | Hydrophobic |
| C1D | CD2 | LEU- 97 | 4.07 | 0 | Hydrophobic |
| C2D | CB | LEU- 97 | 4.17 | 0 | Hydrophobic |
| N6A | OG | SER- 108 | 3.19 | 132.39 | H-Bond (Ligand Donor) |
| O1N | N | PHE- 174 | 2.72 | 159.71 | H-Bond (Protein Donor) |
| C4D | CB | PHE- 174 | 4.13 | 0 | Hydrophobic |
| O2N | N | PHE- 175 | 3.13 | 146.61 | H-Bond (Protein Donor) |
| O2D | OE2 | GLU- 179 | 3 | 161.74 | H-Bond (Ligand Donor) |
| O3D | OE1 | GLU- 179 | 3.16 | 148.38 | H-Bond (Ligand Donor) |
| O3D | OE2 | GLU- 179 | 3.14 | 141.65 | H-Bond (Ligand Donor) |
