sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.490 Å
X-ray
2015-03-24
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.680 | 7.680 | 7.680 | 0.000 | 7.680 | 1 |
| Name: | Serine/threonine-protein kinase/endoribonuclease IRE1 |
|---|---|
| ID: | ERN1_HUMAN |
| AC: | O75460 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 39.810 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.277 | 945.000 |
| % Hydrophobic | % Polar |
|---|---|
| 49.64 | 50.36 |
| According to VolSite | |
| HET Code: | STU |
|---|---|
| Formula: | C28H27N4O3 |
| Molecular weight: | 467.539 g/mol |
| DrugBank ID: | DB02010 |
| Buried Surface Area: | 64.16 % |
| Polar Surface area: | 74.03 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 8 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -18.7583 | 33.5333 | -54.1723 |
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 |
| C25 | CB | LEU- 577 | 4.41 | 0 | Hydrophobic |
| C19 | CB | LEU- 577 | 4.21 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 577 | 4.32 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 577 | 4.05 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 577 | 3.97 | 0 | Hydrophobic |
| C20 | CB | LEU- 577 | 3.73 | 0 | Hydrophobic |
| C25 | CG1 | VAL- 586 | 4.43 | 0 | Hydrophobic |
| C17 | CG1 | VAL- 586 | 4.11 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 586 | 3.9 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 586 | 3.8 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 586 | 3.98 | 0 | Hydrophobic |
| C10 | CB | ALA- 597 | 4.28 | 0 | Hydrophobic |
| C14 | CD | LYS- 599 | 3.47 | 0 | Hydrophobic |
| C13 | CD1 | ILE- 642 | 3.5 | 0 | Hydrophobic |
| N1 | O | GLU- 643 | 2.69 | 174.86 | H-Bond (Ligand Donor) |
| O5 | N | CYS- 645 | 2.57 | 156.13 | H-Bond (Protein Donor) |
| C24 | CG2 | THR- 648 | 3.73 | 0 | Hydrophobic |
| C1 | CG2 | THR- 648 | 3.98 | 0 | Hydrophobic |
| N4 | O | HIS- 692 | 3 | 150.03 | H-Bond (Ligand Donor) |
| C19 | CD2 | LEU- 695 | 4.31 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 695 | 4.25 | 0 | Hydrophobic |
| C27 | CD2 | LEU- 695 | 4.04 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 695 | 3.5 | 0 | Hydrophobic |
| C27 | CB | ASP- 711 | 4.35 | 0 | Hydrophobic |
| C15 | CB | ASP- 711 | 3.99 | 0 | Hydrophobic |
