sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.010 Å
X-ray
2012-03-22
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.620 | 9.620 | 9.620 | 0.000 | 9.620 | 1 |
| 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 |
|---|---|
| B | 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) |
|---|---|
| 1.651 | 722.250 |
| % Hydrophobic | % Polar |
|---|---|
| 65.89 | 34.11 |
| According to VolSite | |
| HET Code: | 0NN |
|---|---|
| Formula: | C27H37N3O2 |
| Molecular weight: | 435.602 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.84 % |
| Polar Surface area: | 47.21 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 15.1386 | -39.6379 | 36.8711 |
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 |
| N2 | OE1 | GLN- 107 | 3.03 | 145.29 | H-Bond (Ligand Donor) |
| C19 | CB | ASP- 110 | 3.64 | 0 | Hydrophobic |
| C22 | CG1 | VAL- 126 | 4.44 | 0 | Hydrophobic |
| C25 | CG1 | ILE- 127 | 3.61 | 0 | Hydrophobic |
| N1 | OD1 | ASP- 130 | 3.66 | 0 | Ionic (Ligand Cationic) |
| N1 | OD2 | ASP- 130 | 2.73 | 0 | Ionic (Ligand Cationic) |
| N1 | OD2 | ASP- 130 | 2.73 | 163.28 | H-Bond (Ligand Donor) |
| C24 | CB | ASP- 130 | 4.23 | 0 | Hydrophobic |
| C9 | CZ | TYR- 131 | 4.38 | 0 | Hydrophobic |
| C3 | CB | TYR- 131 | 4.43 | 0 | Hydrophobic |
| C1 | CE | MET- 134 | 4.3 | 0 | Hydrophobic |
| C11 | CE | MET- 134 | 3.86 | 0 | Hydrophobic |
| C4 | CG | MET- 134 | 3.67 | 0 | Hydrophobic |
| C3 | CB | MET- 134 | 3.3 | 0 | Hydrophobic |
| C27 | SG | CYS- 200 | 4.16 | 0 | Hydrophobic |
| C3 | CG2 | ILE- 219 | 4.27 | 0 | Hydrophobic |
| C5 | CG2 | ILE- 219 | 3.48 | 0 | Hydrophobic |
| C4 | CB | SER- 223 | 3.83 | 0 | Hydrophobic |
| C11 | CZ3 | TRP- 276 | 4.11 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 279 | 4.43 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 283 | 3.56 | 0 | Hydrophobic |
| C14 | CG2 | THR- 305 | 4.39 | 0 | Hydrophobic |
| C14 | CZ | TYR- 309 | 4.37 | 0 | Hydrophobic |
