sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.450 Å
X-ray
2004-03-19
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.730 | 9.060 | 9.060 | 0.340 | 9.400 | 2 |
| Name: | Progesterone receptor |
|---|---|
| ID: | PRGR_HUMAN |
| AC: | P06401 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 20.333 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.543 | 347.625 |
| % Hydrophobic | % Polar |
|---|---|
| 70.87 | 29.13 |
| According to VolSite | |
| HET Code: | NDR |
|---|---|
| Formula: | C20H26O2 |
| Molecular weight: | 298.419 g/mol |
| DrugBank ID: | DB00717 |
| Buried Surface Area: | 78.52 % |
| Polar Surface area: | 37.29 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| -2.45414 | 1.53077 | 25.5553 |
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 |
| C16 | CD2 | LEU- 715 | 3.35 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 718 | 3.95 | 0 | Hydrophobic |
| C13 | CB | LEU- 718 | 4.19 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 721 | 3.79 | 0 | Hydrophobic |
| O22 | NE2 | GLN- 725 | 3 | 125.32 | H-Bond (Protein Donor) |
| C20 | CG | GLN- 725 | 4.45 | 0 | Hydrophobic |
| C7 | CH2 | TRP- 755 | 4.47 | 0 | Hydrophobic |
| C7 | CE | MET- 756 | 3.8 | 0 | Hydrophobic |
| C4 | SD | MET- 756 | 4.05 | 0 | Hydrophobic |
| C3 | SD | MET- 756 | 4.12 | 0 | Hydrophobic |
| C15 | CB | MET- 759 | 4.09 | 0 | Hydrophobic |
| C14 | SD | MET- 759 | 4.18 | 0 | Hydrophobic |
| C15 | CB | VAL- 760 | 4.26 | 0 | Hydrophobic |
| C18 | CD2 | PHE- 778 | 4.39 | 0 | Hydrophobic |
| C16 | CE1 | PHE- 794 | 3.94 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 797 | 3.95 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 797 | 3.89 | 0 | Hydrophobic |
| C9 | SD | MET- 801 | 3.6 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 887 | 4.38 | 0 | Hydrophobic |
| C4 | CG | LEU- 887 | 4.04 | 0 | Hydrophobic |
| C16 | CE1 | TYR- 890 | 3.75 | 0 | Hydrophobic |
| C10 | CD1 | TYR- 890 | 3.79 | 0 | Hydrophobic |
| C7 | SG | CYS- 891 | 3.8 | 0 | Hydrophobic |
| C10 | CB | CYS- 891 | 3.98 | 0 | Hydrophobic |
| C7 | CE | MET- 909 | 3.75 | 0 | Hydrophobic |
| C13 | CE | MET- 909 | 4.25 | 0 | Hydrophobic |
