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: | 18.814 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.440 | 492.750 |
| % Hydrophobic | % Polar |
|---|---|
| 52.05 | 47.95 |
| According to VolSite | |
| HET Code: | 7X8 |
|---|---|
| Formula: | C18H14ClN5O3 |
| Molecular weight: | 383.788 g/mol |
| DrugBank ID: | DB07256 |
| Buried Surface Area: | 64.5 % |
| Polar Surface area: | 111.39 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 10.7561 | 5.79441 | 11.9256 |
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 |
| C5 | CD1 | ILE- 621 | 3.73 | 0 | Hydrophobic |
| C9 | CB | ALA- 645 | 3.39 | 0 | Hydrophobic |
| C12 | CB | ALA- 645 | 4.37 | 0 | Hydrophobic |
| C13 | CB | ALA- 645 | 3.74 | 0 | Hydrophobic |
| C12 | CG | LYS- 647 | 3.91 | 0 | Hydrophobic |
| C13 | CG | LYS- 647 | 4.1 | 0 | Hydrophobic |
| C14 | CD | LYS- 647 | 3.6 | 0 | Hydrophobic |
| C15 | CE | MET- 668 | 4.15 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 677 | 3.73 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 677 | 4.08 | 0 | Hydrophobic |
| C17 | CD1 | ILE- 677 | 4.05 | 0 | Hydrophobic |
| C13 | CG2 | THR- 693 | 3.7 | 0 | Hydrophobic |
| C14 | CG2 | THR- 693 | 3.89 | 0 | Hydrophobic |
| N2 | O | MET- 696 | 2.9 | 146.94 | H-Bond (Ligand Donor) |
| N3 | N | MET- 696 | 3.03 | 150.25 | H-Bond (Protein Donor) |
| C9 | CD1 | LEU- 747 | 3.53 | 0 | Hydrophobic |
| CL1 | CD1 | LEU- 747 | 3.81 | 0 | Hydrophobic |
| CL1 | CB | SER- 757 | 3.9 | 0 | Hydrophobic |
