sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2010-11-24
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.700 | 9.700 | 9.700 | 0.000 | 9.700 | 2 |
| Name: | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 |
|---|---|
| ID: | AT2A1_RABIT |
| AC: | P04191 |
| Organism: | Oryctolagus cuniculus |
| Reign: | Eukaryota |
| TaxID: | 9986 |
| EC Number: | 3.6.3.8 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 55.035 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.641 | 644.625 |
| % Hydrophobic | % Polar |
|---|---|
| 69.63 | 30.37 |
| According to VolSite | |
| HET Code: | TG1 |
|---|---|
| Formula: | C34H50O12 |
| Molecular weight: | 650.754 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.25 % |
| Polar Surface area: | 171.95 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 17 |
| X | Y | Z |
|---|---|---|
| 30.7994 | -23.8803 | 83.6013 |
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 |
| C30 | CD1 | LEU- 253 | 3.67 | 0 | Hydrophobic |
| C25 | CZ | PHE- 256 | 3.77 | 0 | Hydrophobic |
| C26 | CE1 | PHE- 256 | 3.89 | 0 | Hydrophobic |
| C6 | CD1 | PHE- 256 | 3.77 | 0 | Hydrophobic |
| C31 | CE1 | PHE- 256 | 4.19 | 0 | Hydrophobic |
| C28 | CD1 | PHE- 256 | 4.06 | 0 | Hydrophobic |
| C30 | CB | PHE- 256 | 3.55 | 0 | Hydrophobic |
| C26 | CB | GLN- 259 | 3.87 | 0 | Hydrophobic |
| C25 | CD1 | LEU- 260 | 3.7 | 0 | Hydrophobic |
| C26 | CB | LEU- 260 | 3.86 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 263 | 4.15 | 0 | Hydrophobic |
| C26 | CG2 | VAL- 263 | 4.26 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 267 | 3.75 | 0 | Hydrophobic |
| C25 | CG2 | ILE- 765 | 4.49 | 0 | Hydrophobic |
| C31 | CG2 | ILE- 765 | 3.41 | 0 | Hydrophobic |
| C28 | CD1 | ILE- 765 | 3.68 | 0 | Hydrophobic |
| C25 | CB | ASN- 768 | 4.02 | 0 | Hydrophobic |
| C25 | CG2 | VAL- 769 | 4.32 | 0 | Hydrophobic |
| C31 | CG2 | VAL- 769 | 4.23 | 0 | Hydrophobic |
| C33 | CG2 | VAL- 769 | 4.43 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 772 | 3.68 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 772 | 3.47 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 773 | 4.42 | 0 | Hydrophobic |
| C19 | CD2 | PHE- 776 | 4.39 | 0 | Hydrophobic |
| C20 | CB | PHE- 776 | 3.66 | 0 | Hydrophobic |
| C28 | CB | LEU- 828 | 4.35 | 0 | Hydrophobic |
| C29 | CD2 | LEU- 828 | 3.96 | 0 | Hydrophobic |
| C8 | CB | ILE- 829 | 4.04 | 0 | Hydrophobic |
| C9 | CG2 | ILE- 829 | 3.71 | 0 | Hydrophobic |
| C28 | CD1 | ILE- 829 | 4.41 | 0 | Hydrophobic |
| C1 | CE2 | PHE- 834 | 4.24 | 0 | Hydrophobic |
| C14 | CZ | PHE- 834 | 3.78 | 0 | Hydrophobic |
| C33 | CE1 | PHE- 834 | 4.02 | 0 | Hydrophobic |
| C9 | CE2 | PHE- 834 | 3.98 | 0 | Hydrophobic |
| C33 | CB | TYR- 837 | 3.68 | 0 | Hydrophobic |
| C16 | CE | MET- 838 | 4.1 | 0 | Hydrophobic |
| C33 | CG | MET- 838 | 3.73 | 0 | Hydrophobic |
| C15 | CE | MET- 838 | 4.32 | 0 | Hydrophobic |
| O11 | O | HOH- 2148 | 2.63 | 160.51 | H-Bond (Ligand Donor) |
