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
2015-08-30
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.140 | 9.140 | 9.140 | 0.000 | 9.140 | 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 |
|---|---|
| A | 100 % |
| B-Factor: | 0.000 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.652 | 945.000 |
| % Hydrophobic | % Polar |
|---|---|
| 62.14 | 37.86 |
| According to VolSite | |
| HET Code: | DGV |
|---|---|
| Formula: | C26H35Cl2N3O |
| Molecular weight: | 476.482 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.08 % |
| Polar Surface area: | 37.98 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -9.04466 | 30.6684 | -2.42431 |
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 |
| CB | CG | GLN- 107 | 4.15 | 0 | Hydrophobic |
| CG | CB | ASP- 110 | 4.05 | 0 | Hydrophobic |
| CG | CZ3 | TRP- 116 | 3.41 | 0 | Hydrophobic |
| CAC | CG1 | VAL- 126 | 4.46 | 0 | Hydrophobic |
| CAA | CG2 | ILE- 127 | 3.72 | 0 | Hydrophobic |
| CAF | CG1 | ILE- 127 | 4.03 | 0 | Hydrophobic |
| NAS | OD2 | ASP- 130 | 2.58 | 159.06 | H-Bond (Ligand Donor) |
| NAS | OD2 | ASP- 130 | 2.58 | 0 | Ionic (Ligand Cationic) |
| NAS | OD1 | ASP- 130 | 3.92 | 0 | Ionic (Ligand Cationic) |
| CAB | CB | ASP- 130 | 3.55 | 0 | Hydrophobic |
| CLBC | CG | TYR- 131 | 3.21 | 0 | Hydrophobic |
| CAU | CZ | TYR- 131 | 4.23 | 0 | Hydrophobic |
| CAA | CE1 | TYR- 131 | 3.42 | 0 | Hydrophobic |
| CAZ | CE | MET- 134 | 4.4 | 0 | Hydrophobic |
| CAW | CE | MET- 134 | 3.77 | 0 | Hydrophobic |
| CBE | CG | MET- 134 | 3.46 | 0 | Hydrophobic |
| CBD | CB | MET- 134 | 3.92 | 0 | Hydrophobic |
| CAD | CG2 | VAL- 202 | 4.07 | 0 | Hydrophobic |
| CBF | CG2 | ILE- 219 | 3.34 | 0 | Hydrophobic |
| CBF | CB | SER- 223 | 3.74 | 0 | Hydrophobic |
| CAW | CZ3 | TRP- 276 | 4.03 | 0 | Hydrophobic |
| CLAY | CG1 | VAL- 279 | 3.93 | 0 | Hydrophobic |
| CAW | CG1 | VAL- 279 | 4.25 | 0 | Hydrophobic |
| CLAY | CG | GLN- 280 | 4.34 | 0 | Hydrophobic |
| CLAY | CB | VAL- 283 | 3.4 | 0 | Hydrophobic |
