sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2000-06-19
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.310 | 9.310 | 9.310 | 0.000 | 9.310 | 1 |
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 21.553 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.689 | 354.375 |
| % Hydrophobic | % Polar |
|---|---|
| 76.19 | 23.81 |
| According to VolSite | |
| HET Code: | R18 |
|---|---|
| Formula: | C19H24O2 |
| Molecular weight: | 284.393 g/mol |
| DrugBank ID: | DB02998 |
| Buried Surface Area: | 74.53 % |
| 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 |
|---|---|---|
| 14.1436 | 15.297 | 27.7401 |
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 |
| C27 | CD2 | LEU- 715 | 3.93 | 0 | Hydrophobic |
| C1 | CD2 | LEU- 718 | 3.72 | 0 | Hydrophobic |
| C27 | CB | LEU- 718 | 4.24 | 0 | Hydrophobic |
| O97 | OD1 | ASN- 719 | 2.81 | 152.43 | H-Bond (Ligand Donor) |
| C2 | CD2 | LEU- 721 | 3.83 | 0 | Hydrophobic |
| C18 | CZ3 | TRP- 755 | 3.97 | 0 | Hydrophobic |
| C18 | CE | MET- 756 | 3.98 | 0 | Hydrophobic |
| C8 | SD | MET- 756 | 3.86 | 0 | Hydrophobic |
| C2 | CG | MET- 759 | 3.51 | 0 | Hydrophobic |
| C6 | CB | MET- 759 | 4.24 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 760 | 4.26 | 0 | Hydrophobic |
| C6 | CE1 | PHE- 778 | 4.41 | 0 | Hydrophobic |
| C1 | CD1 | PHE- 778 | 3.97 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 797 | 4.36 | 0 | Hydrophobic |
| C7 | SD | MET- 801 | 4.18 | 0 | Hydrophobic |
| C15 | CB | LEU- 887 | 4.48 | 0 | Hydrophobic |
| C16 | CD2 | TYR- 890 | 3.66 | 0 | Hydrophobic |
| C16 | CB | CYS- 891 | 4.01 | 0 | Hydrophobic |
| C18 | SG | CYS- 891 | 3.67 | 0 | Hydrophobic |
| C18 | CE | MET- 909 | 4.33 | 0 | Hydrophobic |
