sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2008-06-27
| 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: | 38.072 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.982 | 361.125 |
| % Hydrophobic | % Polar |
|---|---|
| 57.94 | 42.06 |
| According to VolSite | |
| HET Code: | 7X3 |
|---|---|
| Formula: | C19H20ClN5O4 |
| Molecular weight: | 417.846 g/mol |
| DrugBank ID: | DB07251 |
| Buried Surface Area: | 50.67 % |
| Polar Surface area: | 99.65 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 10.6728 | 7.56855 | 11.0689 |
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 |
| C21 | CB | ILE- 621 | 4.38 | 0 | Hydrophobic |
| C27 | CD1 | ILE- 621 | 4.37 | 0 | Hydrophobic |
| CL1 | CG1 | ILE- 621 | 3.82 | 0 | Hydrophobic |
| C25 | CD1 | ILE- 621 | 3.93 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 629 | 4.22 | 0 | Hydrophobic |
| CL1 | CG1 | VAL- 629 | 4.15 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 629 | 3.88 | 0 | Hydrophobic |
| C27 | CG1 | VAL- 629 | 3.55 | 0 | Hydrophobic |
| N9 | OG1 | THR- 693 | 3.12 | 150.47 | H-Bond (Protein Donor) |
| C24 | CZ | PHE- 695 | 3.95 | 0 | Hydrophobic |
| N11 | N | MET- 696 | 3.12 | 156.67 | H-Bond (Protein Donor) |
| N13 | O | MET- 696 | 2.92 | 141.47 | H-Bond (Ligand Donor) |
| C18 | CB | ALA- 700 | 4.08 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 747 | 3.98 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 747 | 3.69 | 0 | Hydrophobic |
