sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2003-04-05
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 35.667 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.100 | 830.250 |
| % Hydrophobic | % Polar |
|---|---|
| 58.54 | 41.46 |
| According to VolSite | |
| HET Code: | ROL |
|---|---|
| Formula: | C16H21NO3 |
| Molecular weight: | 275.343 g/mol |
| DrugBank ID: | DB04149 |
| Buried Surface Area: | 64.46 % |
| 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 |
|---|---|---|
| 16.3609 | -2.7096 | -14.0319 |
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 |
| C2 | CE2 | TYR- 159 | 4.15 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 319 | 4.44 | 0 | Hydrophobic |
| C9 | CB | ASN- 321 | 4.4 | 0 | Hydrophobic |
| C16 | CB | ASN- 321 | 3.98 | 0 | Hydrophobic |
| C16 | CE1 | TYR- 329 | 3.94 | 0 | Hydrophobic |
| C16 | CB | TRP- 332 | 4.22 | 0 | Hydrophobic |
| C16 | CB | THR- 333 | 4.3 | 0 | Hydrophobic |
| C8 | CG2 | ILE- 336 | 3.85 | 0 | Hydrophobic |
| C9 | CB | ILE- 336 | 4.49 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 336 | 4.04 | 0 | Hydrophobic |
| C11 | CG1 | ILE- 336 | 4.45 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 336 | 4.11 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 336 | 4.17 | 0 | Hydrophobic |
| C7 | CG1 | ILE- 336 | 3.99 | 0 | Hydrophobic |
| C15 | SD | MET- 337 | 4.2 | 0 | Hydrophobic |
| C15 | CE2 | PHE- 340 | 3.45 | 0 | Hydrophobic |
| C13 | SD | MET- 357 | 3.43 | 0 | Hydrophobic |
| C13 | CB | SER- 368 | 3.78 | 0 | Hydrophobic |
| O3 | NE2 | GLN- 369 | 3.24 | 145.58 | H-Bond (Protein Donor) |
| O2 | NE2 | GLN- 369 | 2.98 | 142.48 | H-Bond (Protein Donor) |
| C3 | CZ | PHE- 372 | 4.31 | 0 | Hydrophobic |
| C11 | CD2 | PHE- 372 | 4.37 | 0 | Hydrophobic |
| C13 | CB | PHE- 372 | 4.06 | 0 | Hydrophobic |
| C12 | CG | PHE- 372 | 3.46 | 0 | Hydrophobic |
| C7 | CE2 | PHE- 372 | 3.46 | 0 | Hydrophobic |
