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
2012-12-07
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.660 | 5.660 | 5.660 | 0.000 | 5.660 | 1 |
| Name: | Ephrin type-B receptor 4 |
|---|---|
| ID: | EPHB4_HUMAN |
| AC: | P54760 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.10.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 53.213 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.165 | 705.375 |
| % Hydrophobic | % Polar |
|---|---|
| 51.67 | 48.33 |
| According to VolSite | |
| HET Code: | STU |
|---|---|
| Formula: | C28H27N4O3 |
| Molecular weight: | 467.539 g/mol |
| DrugBank ID: | DB02010 |
| Buried Surface Area: | 59.48 % |
| 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 |
|---|---|---|
| -0.7338 | -12.666 | 8.03057 |
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 | ILE- 621 | 3.92 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 621 | 3.66 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 621 | 3.52 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 629 | 4.35 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 629 | 4.3 | 0 | Hydrophobic |
| C26 | CG2 | VAL- 629 | 3.82 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 629 | 4.02 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 629 | 3.92 | 0 | Hydrophobic |
| C7 | CB | ALA- 645 | 3.98 | 0 | Hydrophobic |
| N1 | O | GLU- 694 | 2.83 | 167.6 | H-Bond (Ligand Donor) |
| O5 | N | MET- 696 | 2.72 | 147.55 | H-Bond (Protein Donor) |
| C24 | CB | ALA- 700 | 4.49 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 747 | 4.33 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 747 | 4.45 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 747 | 4.46 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 747 | 3.43 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 747 | 3.61 | 0 | Hydrophobic |
| C27 | CB | ASP- 758 | 4.48 | 0 | Hydrophobic |
| C15 | CB | ASP- 758 | 3.81 | 0 | Hydrophobic |
