sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.650 Å
X-ray
2011-06-15
| 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: | 17.089 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.669 | 367.875 |
| % Hydrophobic | % Polar |
|---|---|
| 70.64 | 29.36 |
| According to VolSite | |
| HET Code: | OR8 |
|---|---|
| Formula: | C17H19ClN4O3S |
| Molecular weight: | 394.876 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 81.71 % |
| Polar Surface area: | 98.4 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 10.8297 | 5.05408 | 8.58108 |
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 |
| C24 | CD2 | LEU- 715 | 3.7 | 0 | Hydrophobic |
| C26 | CD1 | LEU- 718 | 4.48 | 0 | Hydrophobic |
| C24 | CB | LEU- 718 | 3.97 | 0 | Hydrophobic |
| C1 | CB | LEU- 718 | 4.39 | 0 | Hydrophobic |
| N13 | OD1 | ASN- 719 | 2.71 | 136.14 | H-Bond (Ligand Donor) |
| C23 | CD2 | LEU- 721 | 3.87 | 0 | Hydrophobic |
| C12 | CH2 | TRP- 755 | 4.13 | 0 | Hydrophobic |
| CL | CE | MET- 756 | 4.06 | 0 | Hydrophobic |
| C4 | SD | MET- 756 | 3.59 | 0 | Hydrophobic |
| C23 | SD | MET- 759 | 4.25 | 0 | Hydrophobic |
| C3 | SD | MET- 759 | 3.71 | 0 | Hydrophobic |
| C22 | CB | VAL- 760 | 4.1 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 763 | 4.43 | 0 | Hydrophobic |
| C26 | CE1 | PHE- 778 | 4.32 | 0 | Hydrophobic |
| CL | CD2 | LEU- 797 | 4.16 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 797 | 4.04 | 0 | Hydrophobic |
| C26 | SD | MET- 801 | 3.51 | 0 | Hydrophobic |
| C22 | SD | MET- 801 | 3.72 | 0 | Hydrophobic |
| CL | CB | LEU- 887 | 4.5 | 0 | Hydrophobic |
| CL | CD1 | TYR- 890 | 4.38 | 0 | Hydrophobic |
| C12 | SG | CYS- 891 | 4.12 | 0 | Hydrophobic |
| C12 | CE2 | PHE- 905 | 4.38 | 0 | Hydrophobic |
| C12 | SD | MET- 909 | 3.65 | 0 | Hydrophobic |
| C5 | CE | MET- 909 | 4.25 | 0 | Hydrophobic |
