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: | 65.366 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.721 | 702.000 |
| % Hydrophobic | % Polar |
|---|---|
| 69.23 | 30.77 |
| According to VolSite | |
| HET Code: | TG1 |
|---|---|
| Formula: | C34H50O12 |
| Molecular weight: | 650.754 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.22 % |
| 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 |
|---|---|---|
| 30.9912 | -24.0947 | 83.8606 |
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 | 3.56 | 0 | Hydrophobic |
| C25 | CZ | PHE- 256 | 3.9 | 0 | Hydrophobic |
| C26 | CE1 | PHE- 256 | 3.64 | 0 | Hydrophobic |
| C6 | CD1 | PHE- 256 | 3.76 | 0 | Hydrophobic |
| C31 | CE1 | PHE- 256 | 3.81 | 0 | Hydrophobic |
| C28 | CD1 | PHE- 256 | 4.33 | 0 | Hydrophobic |
| C30 | CB | PHE- 256 | 3.62 | 0 | Hydrophobic |
| C26 | CB | GLN- 259 | 3.94 | 0 | Hydrophobic |
| C25 | CD1 | LEU- 260 | 3.38 | 0 | Hydrophobic |
| C26 | CB | LEU- 260 | 3.9 | 0 | Hydrophobic |
| C19 | CD1 | ILE- 267 | 3.78 | 0 | Hydrophobic |
| C28 | CG2 | ILE- 761 | 4.5 | 0 | Hydrophobic |
| C30 | CG2 | ILE- 761 | 4.44 | 0 | Hydrophobic |
| C31 | CG2 | ILE- 765 | 3.27 | 0 | Hydrophobic |
| C30 | CD1 | ILE- 765 | 3.72 | 0 | Hydrophobic |
| C25 | CB | ASN- 768 | 3.93 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 769 | 4.31 | 0 | Hydrophobic |
| C25 | CG2 | VAL- 769 | 4.08 | 0 | Hydrophobic |
| C31 | CG2 | VAL- 769 | 4.37 | 0 | Hydrophobic |
| C33 | CG2 | VAL- 769 | 4.17 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 772 | 3.5 | 0 | Hydrophobic |
| C20 | CG | PHE- 776 | 3.62 | 0 | Hydrophobic |
| C28 | CB | LEU- 828 | 4.15 | 0 | Hydrophobic |
| C29 | CD1 | LEU- 828 | 4.04 | 0 | Hydrophobic |
| C31 | CD1 | ILE- 829 | 4.29 | 0 | Hydrophobic |
| C28 | CD1 | ILE- 829 | 3.92 | 0 | Hydrophobic |
| C9 | CB | ILE- 829 | 3.66 | 0 | Hydrophobic |
| O8 | N | ILE- 829 | 3.22 | 123.85 | H-Bond (Protein Donor) |
| C1 | CE2 | PHE- 834 | 4.42 | 0 | Hydrophobic |
| C14 | CZ | PHE- 834 | 4.07 | 0 | Hydrophobic |
| C33 | CB | TYR- 837 | 3.58 | 0 | Hydrophobic |
| C33 | CE | MET- 838 | 3.84 | 0 | Hydrophobic |
| C14 | CE | MET- 838 | 3.5 | 0 | Hydrophobic |
| O11 | O | HOH- 4214 | 2.94 | 163.78 | H-Bond (Ligand Donor) |
