sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.950 Å
X-ray
2009-02-03
| 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: | 27.739 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.345 | 995.625 |
| % Hydrophobic | % Polar |
|---|---|
| 56.27 | 43.73 |
| According to VolSite | |
| HET Code: | ROL |
|---|---|
| Formula: | C16H21NO3 |
| Molecular weight: | 275.343 g/mol |
| DrugBank ID: | DB04149 |
| Buried Surface Area: | 67.59 % |
| 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 |
|---|---|---|
| 16.8686 | -3.10945 | -13.1333 |
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- 325 | 4.39 | 0 | Hydrophobic |
| O1 | NE2 | HIS- 326 | 2.7 | 165.13 | H-Bond (Protein Donor) |
| C16 | CB | ASN- 487 | 4.21 | 0 | Hydrophobic |
| C16 | CE1 | TYR- 495 | 3.89 | 0 | Hydrophobic |
| C16 | CB | TRP- 498 | 4.11 | 0 | Hydrophobic |
| C16 | CB | THR- 499 | 4.22 | 0 | Hydrophobic |
| C8 | CG2 | ILE- 502 | 3.78 | 0 | Hydrophobic |
| C9 | CG1 | ILE- 502 | 4.46 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 502 | 3.99 | 0 | Hydrophobic |
| C11 | CG1 | ILE- 502 | 4.21 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 502 | 4.1 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 502 | 3.88 | 0 | Hydrophobic |
| C6 | CG1 | ILE- 502 | 3.88 | 0 | Hydrophobic |
| C15 | SD | MET- 503 | 3.69 | 0 | Hydrophobic |
| C15 | CE2 | PHE- 506 | 3.85 | 0 | Hydrophobic |
| C13 | SD | MET- 523 | 3.53 | 0 | Hydrophobic |
| C14 | CB | SER- 534 | 3.55 | 0 | Hydrophobic |
| O3 | NE2 | GLN- 535 | 3.22 | 140.95 | H-Bond (Protein Donor) |
| O2 | NE2 | GLN- 535 | 2.9 | 141.46 | H-Bond (Protein Donor) |
| C3 | CZ | PHE- 538 | 4.41 | 0 | Hydrophobic |
| C13 | CB | PHE- 538 | 3.62 | 0 | Hydrophobic |
| C12 | CG | PHE- 538 | 3.88 | 0 | Hydrophobic |
