sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
2015-08-31
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.600 | 9.600 | 9.600 | 0.000 | 9.600 | 2 |
| Name: | Nociceptin receptor |
|---|---|
| ID: | OPRX_HUMAN |
| AC: | P41146 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 0.000 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.343 | 1350.000 |
| % Hydrophobic | % Polar |
|---|---|
| 47.50 | 52.50 |
| According to VolSite | |
| HET Code: | DGW |
|---|---|
| Formula: | C24H30Cl2NO |
| Molecular weight: | 419.407 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.06 % |
| Polar Surface area: | 24.67 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -9.22646 | 29.0429 | -2.70832 |
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 |
| CAA | CB | GLN- 107 | 3.96 | 0 | Hydrophobic |
| CAS | CG | GLN- 107 | 4.08 | 0 | Hydrophobic |
| CAG | CB | ASP- 110 | 4.13 | 0 | Hydrophobic |
| CAA | CB | ASP- 110 | 4.37 | 0 | Hydrophobic |
| CAA | CG1 | ILE- 111 | 4 | 0 | Hydrophobic |
| CLAD | CB | ASP- 130 | 4.36 | 0 | Hydrophobic |
| NBB | OD2 | ASP- 130 | 2.78 | 143.11 | H-Bond (Ligand Donor) |
| NBB | OD2 | ASP- 130 | 2.78 | 0 | Ionic (Ligand Cationic) |
| CLAD | CE2 | TYR- 131 | 3.46 | 0 | Hydrophobic |
| CAM | CE | MET- 134 | 4.36 | 0 | Hydrophobic |
| CAE | CG | MET- 134 | 4.05 | 0 | Hydrophobic |
| CAT | CE | MET- 134 | 4.32 | 0 | Hydrophobic |
| CAF | CB | CYS- 200 | 3.74 | 0 | Hydrophobic |
| CAE | CG2 | ILE- 219 | 3.34 | 0 | Hydrophobic |
| CAM | CZ3 | TRP- 276 | 4.38 | 0 | Hydrophobic |
| CLAC | CG1 | VAL- 279 | 3.44 | 0 | Hydrophobic |
| CLAC | CG | GLN- 280 | 4.39 | 0 | Hydrophobic |
| CAH | CG | GLN- 280 | 4.27 | 0 | Hydrophobic |
| CLAC | CG2 | VAL- 283 | 3.32 | 0 | Hydrophobic |
| CAT | CG1 | VAL- 283 | 4.24 | 0 | Hydrophobic |
| CAN | CG2 | VAL- 283 | 4.08 | 0 | Hydrophobic |
| CAL | CG2 | THR- 305 | 4.3 | 0 | Hydrophobic |
