sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2012-10-30
| Name: | 2',3'-cyclic-nucleotide 3'-phosphodiesterase |
|---|---|
| ID: | CN37_MOUSE |
| AC: | P16330 |
| Organism: | Mus musculus |
| Reign: | Eukaryota |
| TaxID: | 10090 |
| EC Number: | 3.1.4.37 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 44.299 |
|---|---|
| Number of residues: | 21 |
| Including | |
| Standard Amino Acids: | 19 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.089 | 874.125 |
| % Hydrophobic | % Polar |
|---|---|
| 48.26 | 51.74 |
| According to VolSite | |
| HET Code: | QQY |
|---|---|
| Formula: | C10H11N5O5PS |
| Molecular weight: | 344.264 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 42.43 % |
| Polar Surface area: | 164.32 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -8.56586 | 4.20291 | -24.1734 |
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 |
| C5' | CE2 | TYR- 168 | 3.38 | 0 | Hydrophobic |
| O3' | OG1 | THR- 232 | 2.74 | 161.24 | H-Bond (Protein Donor) |
| C1' | CD1 | PHE- 235 | 4.14 | 0 | Hydrophobic |
| OP3 | NE2 | HIS- 309 | 2.85 | 175.96 | H-Bond (Ligand Donor) |
| C3' | CB | PRO- 320 | 4.45 | 0 | Hydrophobic |
| C2' | CG | PRO- 320 | 4.03 | 0 | Hydrophobic |
