sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2012-08-10
| Name: | Ephrin type-A receptor 3 |
|---|---|
| ID: | EPHA3_HUMAN |
| AC: | P29320 |
| 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: | 27.071 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.965 | 712.125 |
| % Hydrophobic | % Polar |
|---|---|
| 45.97 | 54.03 |
| According to VolSite | |
| HET Code: | L90 |
|---|---|
| Formula: | C20H21N7O2 |
| Molecular weight: | 391.426 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.36 % |
| Polar Surface area: | 100.32 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -8.91428 | 7.29224 | 51.3802 |
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 |
| C18 | CG1 | VAL- 627 | 4.25 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 635 | 4.24 | 0 | Hydrophobic |
| C26 | CB | ALA- 651 | 3.82 | 0 | Hydrophobic |
| C6 | CD | LYS- 653 | 4.08 | 0 | Hydrophobic |
| C12 | CG | LYS- 653 | 3.82 | 0 | Hydrophobic |
| C26 | CG | LYS- 653 | 3.45 | 0 | Hydrophobic |
| C11 | CD | LYS- 653 | 3.24 | 0 | Hydrophobic |
| N27 | OE2 | GLU- 670 | 2.61 | 160.41 | H-Bond (Ligand Donor) |
| C13 | CG | GLU- 670 | 4.29 | 0 | Hydrophobic |
| C13 | CE | MET- 674 | 3.28 | 0 | Hydrophobic |
| C12 | CG2 | ILE- 697 | 3.52 | 0 | Hydrophobic |
| C26 | CG2 | THR- 699 | 3.86 | 0 | Hydrophobic |
| C12 | CG2 | THR- 699 | 3.35 | 0 | Hydrophobic |
| O3 | N | MET- 702 | 2.87 | 151.03 | H-Bond (Protein Donor) |
| C8 | CD1 | LEU- 753 | 3.76 | 0 | Hydrophobic |
| C9 | CB | SER- 763 | 3.8 | 0 | Hydrophobic |
| C9 | CB | ASP- 764 | 4.2 | 0 | Hydrophobic |
| N28 | N | ASP- 764 | 2.79 | 148.46 | H-Bond (Protein Donor) |
