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
2007-11-07
| 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: | 71.302 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | CA |
| Ligandability | Volume (Å3) |
|---|---|
| 0.121 | 2666.250 |
| % Hydrophobic | % Polar |
|---|---|
| 40.51 | 59.49 |
| According to VolSite | |
| HET Code: | AN2 |
|---|---|
| Formula: | C10H14N6O9P2 |
| Molecular weight: | 424.200 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.58 % |
| Polar Surface area: | 263.66 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 13 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -17.3594 | 0.572593 | 8.98589 |
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 |
| N3B | OG1 | THR- 353 | 2.55 | 129.66 | H-Bond (Ligand Donor) |
| C8 | CG2 | THR- 441 | 4.5 | 0 | Hydrophobic |
| N6 | OE2 | GLU- 442 | 3.47 | 140.26 | H-Bond (Ligand Donor) |
| C1' | CE2 | PHE- 487 | 3.8 | 0 | Hydrophobic |
| C8 | CZ | PHE- 487 | 3.56 | 0 | Hydrophobic |
| C5 | CB | PHE- 487 | 4.41 | 0 | Hydrophobic |
| C5' | CZ | PHE- 487 | 4.42 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 487 | 3.72 | 0 | Aromatic Face/Face |
| O2A | CZ | ARG- 489 | 3.41 | 0 | Ionic (Protein Cationic) |
| C4' | CB | LYS- 492 | 4.37 | 0 | Hydrophobic |
| C4' | CB | ALA- 517 | 4.19 | 0 | Hydrophobic |
| C1' | CB | ALA- 517 | 4.28 | 0 | Hydrophobic |
| O1B | NH2 | ARG- 560 | 2.58 | 150.9 | H-Bond (Protein Donor) |
| O1B | CZ | ARG- 560 | 3.48 | 0 | Ionic (Protein Cationic) |
| C2' | CD1 | LEU- 562 | 3.68 | 0 | Hydrophobic |
| N3B | OG1 | THR- 625 | 2.86 | 135.31 | H-Bond (Ligand Donor) |
| O2' | O | HOH- 1050 | 2.52 | 179.95 | H-Bond (Protein Donor) |
