sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2008-12-08
| 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: | 99.999 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.426 | 1184.625 |
| % Hydrophobic | % Polar |
|---|---|
| 56.13 | 43.87 |
| According to VolSite | |
| HET Code: | CZA |
|---|---|
| Formula: | C20H20N2O3 |
| Molecular weight: | 336.384 g/mol |
| DrugBank ID: | DB07604 |
| Buried Surface Area: | 69.88 % |
| Polar Surface area: | 77.42 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 38.9939 | 58.6828 | 12.5547 |
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 |
| C1 | CB | GLN- 56 | 4.34 | 0 | Hydrophobic |
| C1 | CE1 | PHE- 57 | 4.15 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 61 | 3.92 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 61 | 3.52 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 61 | 4.18 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 62 | 3.89 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 62 | 3.48 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 62 | 4.16 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 65 | 3.87 | 0 | Hydrophobic |
| C1 | CB | ASN- 101 | 3.92 | 0 | Hydrophobic |
| C1 | CB | ALA- 102 | 3.96 | 0 | Hydrophobic |
| C18 | CB | LEU- 253 | 4.11 | 0 | Hydrophobic |
| C10 | CG2 | ILE- 307 | 3.59 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 307 | 3.88 | 0 | Hydrophobic |
| C8 | CG2 | ILE- 307 | 4.03 | 0 | Hydrophobic |
| C11 | CB | GLU- 309 | 3.9 | 0 | Hydrophobic |
| C20 | CD1 | LEU- 311 | 3.29 | 0 | Hydrophobic |
| C12 | CG | PRO- 312 | 3.91 | 0 | Hydrophobic |
| C11 | CG | PRO- 312 | 3.96 | 0 | Hydrophobic |
| O2 | MN | MN- 1006 | 2.15 | 0 | Metal Acceptor |
| O1 | MN | MN- 1006 | 2.26 | 0 | Metal Acceptor |
