sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.030 Å
X-ray
2014-12-09
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.140 | 8.790 | 8.790 | 0.650 | 9.440 | 2 |
| Name: | Mineralocorticoid receptor |
|---|---|
| ID: | MCR_HUMAN |
| AC: | P08235 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 21.916 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.513 | 337.500 |
| % Hydrophobic | % Polar |
|---|---|
| 66.00 | 34.00 |
| According to VolSite | |
| HET Code: | DEX |
|---|---|
| Formula: | C22H29FO5 |
| Molecular weight: | 392.461 g/mol |
| DrugBank ID: | DB01234 |
| Buried Surface Area: | 85.55 % |
| Polar Surface area: | 94.83 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -2.92818 | -15.7734 | -0.570321 |
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 |
| C21 | CB | LEU- 766 | 3.95 | 0 | Hydrophobic |
| F1 | CD1 | LEU- 769 | 4.01 | 0 | Hydrophobic |
| C11 | CB | LEU- 769 | 3.71 | 0 | Hydrophobic |
| O2 | OD1 | ASN- 770 | 2.92 | 165.71 | H-Bond (Ligand Donor) |
| O5 | ND2 | ASN- 770 | 3.14 | 163.28 | H-Bond (Protein Donor) |
| C19 | CB | ALA- 773 | 3.6 | 0 | Hydrophobic |
| O1 | NE2 | GLN- 776 | 3.14 | 151.57 | H-Bond (Protein Donor) |
| C18 | CH2 | TRP- 806 | 4.31 | 0 | Hydrophobic |
| C19 | CZ3 | TRP- 806 | 3.83 | 0 | Hydrophobic |
| C18 | CE | MET- 807 | 3.95 | 0 | Hydrophobic |
| C7 | SD | MET- 807 | 3.89 | 0 | Hydrophobic |
| C15 | CE | MET- 807 | 3.75 | 0 | Hydrophobic |
| C6 | CB | SER- 810 | 3.99 | 0 | Hydrophobic |
| C19 | CB | SER- 810 | 3.66 | 0 | Hydrophobic |
| O1 | NH2 | ARG- 817 | 2.87 | 123.97 | H-Bond (Protein Donor) |
| F1 | CE1 | PHE- 829 | 3.37 | 0 | Hydrophobic |
| C22 | SD | MET- 845 | 3.63 | 0 | Hydrophobic |
| C22 | CD1 | LEU- 848 | 3.81 | 0 | Hydrophobic |
| C7 | SD | MET- 852 | 3.67 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 938 | 3.97 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 938 | 4.26 | 0 | Hydrophobic |
| C22 | CD1 | PHE- 941 | 3.53 | 0 | Hydrophobic |
| C16 | CB | CYS- 942 | 4.38 | 0 | Hydrophobic |
| C18 | SG | CYS- 942 | 4.16 | 0 | Hydrophobic |
| O5 | OG1 | THR- 945 | 2.85 | 147.81 | H-Bond (Ligand Donor) |
| C21 | CG1 | VAL- 954 | 4.39 | 0 | Hydrophobic |
