sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.650 Å
X-ray
2008-06-30
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 17.919 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.484 | 475.875 |
| % Hydrophobic | % Polar |
|---|---|
| 58.16 | 41.84 |
| According to VolSite | |
| HET Code: | 7X6 |
|---|---|
| Formula: | C18H16ClN5O4S |
| Molecular weight: | 433.869 g/mol |
| DrugBank ID: | DB07254 |
| Buried Surface Area: | 65.75 % |
| Polar Surface area: | 122.85 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 10.5037 | 5.96338 | 11.7348 |
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 |
| C6 | CD1 | ILE- 621 | 3.61 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 629 | 4.46 | 0 | Hydrophobic |
| C9 | CB | ALA- 645 | 3.39 | 0 | Hydrophobic |
| C12 | CB | ALA- 645 | 4.4 | 0 | Hydrophobic |
| C13 | CB | ALA- 645 | 3.84 | 0 | Hydrophobic |
| C12 | CG | LYS- 647 | 3.86 | 0 | Hydrophobic |
| C13 | CG | LYS- 647 | 3.92 | 0 | Hydrophobic |
| C14 | CD | LYS- 647 | 3.64 | 0 | Hydrophobic |
| C15 | CE | MET- 668 | 4.12 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 677 | 3.67 | 0 | Hydrophobic |
| C17 | CD1 | ILE- 677 | 4.34 | 0 | Hydrophobic |
| C13 | CG2 | THR- 693 | 3.78 | 0 | Hydrophobic |
| C14 | CG2 | THR- 693 | 3.95 | 0 | Hydrophobic |
| N2 | O | MET- 696 | 2.91 | 141.17 | H-Bond (Ligand Donor) |
| N3 | N | MET- 696 | 2.99 | 157.03 | H-Bond (Protein Donor) |
| C1 | CB | ALA- 700 | 4.14 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 747 | 3.47 | 0 | Hydrophobic |
| CL1 | CD1 | LEU- 747 | 3.83 | 0 | Hydrophobic |
| C1 | CD2 | LEU- 747 | 4.25 | 0 | Hydrophobic |
| CL1 | CB | SER- 757 | 3.95 | 0 | Hydrophobic |
