sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2003-08-25
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.070 | 6.290 | 6.420 | 0.600 | 7.230 | 7 |
| Name: | cAMP-specific 3',5'-cyclic phosphodiesterase 4D |
|---|---|
| ID: | PDE4D_HUMAN |
| AC: | Q08499 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.1.4.53 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 28.076 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.122 | 857.250 |
| % Hydrophobic | % Polar |
|---|---|
| 54.72 | 45.28 |
| According to VolSite | |
| HET Code: | ROL |
|---|---|
| Formula: | C16H21NO3 |
| Molecular weight: | 275.343 g/mol |
| DrugBank ID: | DB04149 |
| Buried Surface Area: | 63.19 % |
| Polar Surface area: | 47.56 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 21.4799 | -4.4894 | 31.8872 |
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 |
| C3 | CD2 | LEU- 319 | 4.29 | 0 | Hydrophobic |
| C9 | CB | ASN- 321 | 4.44 | 0 | Hydrophobic |
| C16 | CB | ASN- 321 | 4.01 | 0 | Hydrophobic |
| C16 | CG | PRO- 322 | 4.49 | 0 | Hydrophobic |
| C16 | CE1 | TYR- 329 | 3.52 | 0 | Hydrophobic |
| C8 | CG2 | ILE- 336 | 3.64 | 0 | Hydrophobic |
| C9 | CB | ILE- 336 | 4.34 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 336 | 4.44 | 0 | Hydrophobic |
| C7 | CG1 | ILE- 336 | 3.63 | 0 | Hydrophobic |
| C15 | CG1 | ILE- 336 | 3.95 | 0 | Hydrophobic |
| C14 | SD | MET- 337 | 3.99 | 0 | Hydrophobic |
| C15 | CE2 | PHE- 340 | 3.47 | 0 | Hydrophobic |
| C14 | SD | MET- 357 | 3.42 | 0 | Hydrophobic |
| C13 | CB | SER- 368 | 3.93 | 0 | Hydrophobic |
| O3 | NE2 | GLN- 369 | 3.23 | 144.91 | H-Bond (Protein Donor) |
| O2 | NE2 | GLN- 369 | 3.2 | 142.23 | H-Bond (Protein Donor) |
| C2 | CZ | PHE- 372 | 4.44 | 0 | Hydrophobic |
| C13 | CB | PHE- 372 | 4.08 | 0 | Hydrophobic |
| C12 | CG | PHE- 372 | 3.55 | 0 | Hydrophobic |
| C16 | CE2 | PHE- 372 | 4.23 | 0 | Hydrophobic |
