sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2015-06-15
| Name: | Mu-type opioid receptor |
|---|---|
| ID: | OPRM_MOUSE |
| AC: | P42866 |
| Organism: | Mus musculus |
| Reign: | Eukaryota |
| TaxID: | 10090 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| A | 100 % |
| B-Factor: | 57.326 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.237 | 1211.625 |
| % Hydrophobic | % Polar |
|---|---|
| 50.70 | 49.30 |
| According to VolSite | |
| HET Code: | CLR |
|---|---|
| Formula: | C27H46O |
| Molecular weight: | 386.654 g/mol |
| DrugBank ID: | DB04540 |
| Buried Surface Area: | 38.23 % |
| Polar Surface area: | 20.23 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -14.0507 | 14.119 | -62.5865 |
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 | ND1 | HIS- 54 | 3.41 | 148.7 | H-Bond (Ligand Donor) |
| CAJ | CB | SER- 55 | 3.53 | 0 | Hydrophobic |
| CAG | CG | GLN- 124 | 4.02 | 0 | Hydrophobic |
| CAG | CG1 | VAL- 143 | 4.04 | 0 | Hydrophobic |
| CAI | CG1 | ILE- 144 | 4.22 | 0 | Hydrophobic |
| NBB | OD2 | ASP- 147 | 2.66 | 137.02 | H-Bond (Ligand Donor) |
| NBB | OD2 | ASP- 147 | 2.66 | 0 | Ionic (Ligand Cationic) |
| NBB | OD1 | ASP- 147 | 3.89 | 0 | Ionic (Ligand Cationic) |
| CAI | CB | ASP- 147 | 3.98 | 0 | Hydrophobic |
| CAP | CZ | TYR- 148 | 3.7 | 0 | Hydrophobic |
| CAM | CE | MET- 151 | 3.91 | 0 | Hydrophobic |
| CAQ | SD | MET- 151 | 4.21 | 0 | Hydrophobic |
| CAL | CG1 | VAL- 236 | 3.63 | 0 | Hydrophobic |
| CAQ | CZ3 | TRP- 293 | 4.04 | 0 | Hydrophobic |
| CAF | CD1 | ILE- 296 | 4.47 | 0 | Hydrophobic |
| CAE | CG1 | ILE- 296 | 4.02 | 0 | Hydrophobic |
| CAM | CG1 | ILE- 296 | 4.35 | 0 | Hydrophobic |
| CAU | CG2 | VAL- 300 | 4.06 | 0 | Hydrophobic |
| CAA | CZ2 | TRP- 318 | 3.93 | 0 | Hydrophobic |
| CAF | CZ2 | TRP- 318 | 4.17 | 0 | Hydrophobic |
| CAC | CD1 | ILE- 322 | 3.98 | 0 | Hydrophobic |
| CAF | CG1 | ILE- 322 | 4.36 | 0 | Hydrophobic |
| NBB | OH | TYR- 326 | 3.24 | 123.15 | H-Bond (Ligand Donor) |
