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
2003-12-01
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.830 | 6.450 | 6.660 | 0.360 | 6.660 | 4 |
| Name: | cAMP-specific 3',5'-cyclic phosphodiesterase 4B |
|---|---|
| ID: | PDE4B_HUMAN |
| AC: | Q07343 |
| 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: | 34.187 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN MN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.137 | 843.750 |
| % Hydrophobic | % Polar |
|---|---|
| 56.40 | 43.60 |
| According to VolSite | |
| HET Code: | ROL |
|---|---|
| Formula: | C16H21NO3 |
| Molecular weight: | 275.343 g/mol |
| DrugBank ID: | DB04149 |
| Buried Surface Area: | 65.98 % |
| 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 |
|---|---|---|
| 19.9221 | 111.019 | 29.3028 |
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- 233 | 3.77 | 0 | Hydrophobic |
| O1 | NE2 | HIS- 234 | 2.76 | 146.12 | H-Bond (Protein Donor) |
| N1 | OD2 | ASP- 392 | 3.04 | 123.84 | H-Bond (Ligand Donor) |
| C3 | CD2 | LEU- 393 | 4.47 | 0 | Hydrophobic |
| C16 | CB | ASN- 395 | 4.48 | 0 | Hydrophobic |
| C16 | CE1 | TYR- 403 | 4.02 | 0 | Hydrophobic |
| C16 | CB | THR- 407 | 4.25 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 410 | 4.32 | 0 | Hydrophobic |
| C8 | CG2 | ILE- 410 | 3.79 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 410 | 4.18 | 0 | Hydrophobic |
| C15 | CG1 | ILE- 410 | 3.99 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 410 | 3.74 | 0 | Hydrophobic |
| C7 | CG1 | ILE- 410 | 3.9 | 0 | Hydrophobic |
| C9 | CG1 | ILE- 410 | 4.28 | 0 | Hydrophobic |
| C14 | SD | MET- 411 | 3.67 | 0 | Hydrophobic |
| C15 | CZ | PHE- 414 | 3.71 | 0 | Hydrophobic |
| C13 | SD | MET- 431 | 3.83 | 0 | Hydrophobic |
| C13 | CB | SER- 442 | 3.36 | 0 | Hydrophobic |
| O3 | NE2 | GLN- 443 | 3.42 | 152.81 | H-Bond (Protein Donor) |
| O2 | NE2 | GLN- 443 | 3.02 | 139.4 | H-Bond (Protein Donor) |
| C11 | CG | PHE- 446 | 4.25 | 0 | Hydrophobic |
| C12 | CB | PHE- 446 | 3.59 | 0 | Hydrophobic |
