sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2014-12-09
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.720 | 8.740 | 8.920 | 0.350 | 9.160 | 16 |
| Name: | Glucocorticoid receptor |
|---|---|
| ID: | GCR_HUMAN |
| AC: | P04150 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 37.622 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.370 | 621.000 |
| % Hydrophobic | % Polar |
|---|---|
| 58.15 | 41.85 |
| According to VolSite | |
| HET Code: | DEX |
|---|---|
| Formula: | C22H29FO5 |
| Molecular weight: | 392.461 g/mol |
| DrugBank ID: | DB01234 |
| Buried Surface Area: | 84.06 % |
| 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 |
|---|---|---|
| -0.464571 | 39.4924 | -10.836 |
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 | CE | MET- 560 | 3.56 | 0 | Hydrophobic |
| C12 | CB | LEU- 563 | 3.93 | 0 | Hydrophobic |
| F1 | CD1 | LEU- 563 | 3.86 | 0 | Hydrophobic |
| C11 | CB | LEU- 563 | 3.73 | 0 | Hydrophobic |
| O2 | OD1 | ASN- 564 | 2.91 | 158.16 | H-Bond (Ligand Donor) |
| O5 | ND2 | ASN- 564 | 3.3 | 164.53 | H-Bond (Protein Donor) |
| O1 | NE2 | GLN- 570 | 3.22 | 137.45 | H-Bond (Protein Donor) |
| C19 | CZ3 | TRP- 600 | 3.94 | 0 | Hydrophobic |
| C18 | CE | MET- 601 | 4.04 | 0 | Hydrophobic |
| C7 | SD | MET- 601 | 3.78 | 0 | Hydrophobic |
| C15 | CE | MET- 601 | 3.92 | 0 | Hydrophobic |
| C6 | CB | MET- 604 | 3.63 | 0 | Hydrophobic |
| C19 | CB | MET- 604 | 3.91 | 0 | Hydrophobic |
| O1 | NH2 | ARG- 611 | 2.9 | 123.36 | H-Bond (Protein Donor) |
| F1 | CE1 | PHE- 623 | 3.56 | 0 | Hydrophobic |
| C22 | CB | GLN- 642 | 3.66 | 0 | Hydrophobic |
| O3 | OE1 | GLN- 642 | 3.05 | 152.75 | H-Bond (Ligand Donor) |
| C7 | SD | MET- 646 | 3.95 | 0 | Hydrophobic |
| C22 | CE | MET- 646 | 4.12 | 0 | Hydrophobic |
| F1 | SD | MET- 646 | 4.49 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 732 | 4.41 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 732 | 4.07 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 732 | 4.24 | 0 | Hydrophobic |
| C22 | CB | TYR- 735 | 3.53 | 0 | Hydrophobic |
| C18 | CB | CYS- 736 | 4.12 | 0 | Hydrophobic |
| O5 | OG1 | THR- 739 | 2.8 | 133.68 | H-Bond (Ligand Donor) |
| C18 | CE2 | PHE- 749 | 4.37 | 0 | Hydrophobic |
