sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.400 Å
X-ray
2012-04-06
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.740 | 9.560 | 9.720 | 0.490 | 10.400 | 7 |
| Name: | Delta-type opioid receptor |
|---|---|
| ID: | OPRD_MOUSE |
| AC: | P32300 |
| Organism: | Mus musculus |
| Reign: | Eukaryota |
| TaxID: | 10090 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 0.000 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.383 | 864.000 |
| % Hydrophobic | % Polar |
|---|---|
| 58.20 | 41.80 |
| According to VolSite | |
| HET Code: | EJ4 |
|---|---|
| Formula: | C26H27N2O3 |
| Molecular weight: | 415.504 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 55.63 % |
| Polar Surface area: | 69.92 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 4 |
| Rings: | 8 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 61.9867 | 41.5634 | -10.2713 |
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 |
| NAS | OD2 | ASP- 128 | 2.83 | 140.3 | H-Bond (Ligand Donor) |
| NAS | OD2 | ASP- 128 | 2.83 | 0 | Ionic (Ligand Cationic) |
| NAS | OD1 | ASP- 128 | 3.64 | 0 | Ionic (Ligand Cationic) |
| CAU | CE2 | TYR- 129 | 4 | 0 | Hydrophobic |
| CAU | CE | MET- 132 | 4.1 | 0 | Hydrophobic |
| CAY | SD | MET- 132 | 3.5 | 0 | Hydrophobic |
| CAB | CE | MET- 132 | 3.62 | 0 | Hydrophobic |
| CAZ | CG1 | VAL- 217 | 4.03 | 0 | Hydrophobic |
| CBE | CH2 | TRP- 274 | 3.51 | 0 | Hydrophobic |
| CAO | CD1 | ILE- 277 | 4.24 | 0 | Hydrophobic |
| CBA | CG1 | ILE- 277 | 3.39 | 0 | Hydrophobic |
| CAO | CG2 | VAL- 281 | 3.72 | 0 | Hydrophobic |
| CBA | CG2 | VAL- 281 | 4.35 | 0 | Hydrophobic |
| CAB | CG1 | VAL- 281 | 4.05 | 0 | Hydrophobic |
| CAX | CG2 | VAL- 281 | 3.98 | 0 | Hydrophobic |
| CAI | CG2 | VAL- 281 | 3.53 | 0 | Hydrophobic |
| CAJ | CD1 | LEU- 300 | 3.72 | 0 | Hydrophobic |
| CAI | CD1 | ILE- 304 | 4.21 | 0 | Hydrophobic |
| CBD | CG2 | ILE- 304 | 3.79 | 0 | Hydrophobic |
| CAO | CD1 | ILE- 304 | 3.81 | 0 | Hydrophobic |
| CBC | CZ | TYR- 308 | 3.74 | 0 | Hydrophobic |
| CBD | CE2 | TYR- 308 | 3.52 | 0 | Hydrophobic |
