sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2012-02-01
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.390 | 10.050 | 10.230 | 0.480 | 10.520 | 3 |
| Name: | Kappa-type opioid receptor |
|---|---|
| ID: | OPRK_HUMAN |
| AC: | P41145 |
| 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: | 37 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.204 | 1005.750 |
| % Hydrophobic | % Polar |
|---|---|
| 39.93 | 60.07 |
| According to VolSite | |
| HET Code: | JDC |
|---|---|
| Formula: | C28H41N3O3 |
| Molecular weight: | 467.643 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.14 % |
| Polar Surface area: | 90.61 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 5 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 3.68409 | -24.0088 | 59.4712 |
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 |
| C3B | CG2 | VAL- 108 | 4.11 | 0 | Hydrophobic |
| C4E | CB | THR- 111 | 4.18 | 0 | Hydrophobic |
| C4E | CB | GLN- 115 | 4.15 | 0 | Hydrophobic |
| C51 | CG2 | VAL- 134 | 4.47 | 0 | Hydrophobic |
| C6C | CG2 | VAL- 134 | 3.44 | 0 | Hydrophobic |
| C5C | CD2 | LEU- 135 | 3.8 | 0 | Hydrophobic |
| N2 | OD1 | ASP- 138 | 3.4 | 125.92 | H-Bond (Ligand Donor) |
| N2 | OD2 | ASP- 138 | 2.77 | 146.08 | H-Bond (Ligand Donor) |
| N11 | OD1 | ASP- 138 | 2.96 | 135.2 | H-Bond (Ligand Donor) |
| N2 | OD1 | ASP- 138 | 3.4 | 0 | Ionic (Ligand Cationic) |
| N2 | OD2 | ASP- 138 | 2.77 | 0 | Ionic (Ligand Cationic) |
| N11 | OD1 | ASP- 138 | 2.96 | 0 | Ionic (Ligand Cationic) |
| C51 | CB | ASP- 138 | 3.55 | 0 | Hydrophobic |
| C4A | SD | MET- 142 | 3.71 | 0 | Hydrophobic |
| C5 | SD | MET- 142 | 3.77 | 0 | Hydrophobic |
| C8A | CE | MET- 142 | 3.86 | 0 | Hydrophobic |
| C4C | CB | CYS- 210 | 3.96 | 0 | Hydrophobic |
| C5C | SG | CYS- 210 | 4.01 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 230 | 3.47 | 0 | Hydrophobic |
| C3D | CH2 | TRP- 287 | 3.54 | 0 | Hydrophobic |
| C4 | CG1 | ILE- 290 | 3.57 | 0 | Hydrophobic |
| C5 | CG1 | ILE- 294 | 3.6 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 294 | 3.6 | 0 | Hydrophobic |
| C3D | CD1 | ILE- 316 | 4.37 | 0 | Hydrophobic |
| C3B | CD1 | TYR- 320 | 3.5 | 0 | Hydrophobic |
