sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.350 Å
X-ray
2013-07-22
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.570 | 9.570 | 9.570 | 0.000 | 9.570 | 1 |
| 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: | 30.036 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.741 | 442.125 |
| % Hydrophobic | % Polar |
|---|---|
| 70.23 | 29.77 |
| According to VolSite | |
| HET Code: | LSJ |
|---|---|
| Formula: | C25H25NO4S |
| Molecular weight: | 435.535 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 81.91 % |
| Polar Surface area: | 73.01 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -8.77906 | 10.7211 | -17.5248 |
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 | SD | MET- 560 | 3.96 | 0 | Hydrophobic |
| C29 | CD1 | LEU- 563 | 4.48 | 0 | Hydrophobic |
| C31 | CD1 | LEU- 563 | 3.54 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 563 | 4.26 | 0 | Hydrophobic |
| N17 | OD1 | ASN- 564 | 2.63 | 136.72 | H-Bond (Ligand Donor) |
| O19 | ND2 | ASN- 564 | 3.12 | 148.53 | H-Bond (Protein Donor) |
| C6 | CD2 | LEU- 566 | 3.74 | 0 | Hydrophobic |
| C7 | CG | GLN- 570 | 4.36 | 0 | Hydrophobic |
| C23 | CZ3 | TRP- 600 | 3.74 | 0 | Hydrophobic |
| C1 | SD | MET- 601 | 4.15 | 0 | Hydrophobic |
| C23 | CE | MET- 601 | 4.15 | 0 | Hydrophobic |
| C12 | CE | MET- 601 | 3.45 | 0 | Hydrophobic |
| C1 | CG | MET- 604 | 4.32 | 0 | Hydrophobic |
| C4 | SD | MET- 604 | 3.71 | 0 | Hydrophobic |
| C8 | CG | MET- 604 | 3.48 | 0 | Hydrophobic |
| C22 | SD | MET- 604 | 3.63 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 608 | 4.32 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 608 | 3.75 | 0 | Hydrophobic |
| C28 | SD | MET- 639 | 4.31 | 0 | Hydrophobic |
| C31 | SD | MET- 639 | 3.59 | 0 | Hydrophobic |
| C27 | CB | GLN- 642 | 4.11 | 0 | Hydrophobic |
| C26 | CG | MET- 646 | 3.94 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 732 | 3.48 | 0 | Hydrophobic |
| C21 | CE1 | TYR- 735 | 3.77 | 0 | Hydrophobic |
| C15 | SG | CYS- 736 | 4.08 | 0 | Hydrophobic |
| C14 | CB | CYS- 736 | 3.44 | 0 | Hydrophobic |
| O20 | OG1 | THR- 739 | 2.71 | 153 | H-Bond (Protein Donor) |
| C23 | CD1 | LEU- 753 | 4.39 | 0 | Hydrophobic |
