sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.710 Å
X-ray
2014-07-01
| 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: | 22.567 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.267 | 367.875 |
| % Hydrophobic | % Polar |
|---|---|
| 65.14 | 34.86 |
| According to VolSite | |
| HET Code: | B96 |
|---|---|
| Formula: | C31H38N5O3 |
| Molecular weight: | 528.665 g/mol |
| DrugBank ID: | DB03044 |
| Buried Surface Area: | 68.26 % |
| Polar Surface area: | 81.85 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 0.332077 | -6.19638 | -15.8996 |
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 |
| C34 | CG1 | VAL- 635 | 4.33 | 0 | Hydrophobic |
| C42 | CG1 | VAL- 635 | 4.34 | 0 | Hydrophobic |
| C34 | CB | ALA- 651 | 3.93 | 0 | Hydrophobic |
| C31 | CD | LYS- 653 | 4.4 | 0 | Hydrophobic |
| C33 | CB | LYS- 653 | 3.48 | 0 | Hydrophobic |
| N9 | OE2 | GLU- 670 | 2.89 | 142.62 | H-Bond (Ligand Donor) |
| C25 | CB | GLU- 670 | 4.27 | 0 | Hydrophobic |
| C21 | CG | GLU- 670 | 3.75 | 0 | Hydrophobic |
| C17 | CG2 | ILE- 673 | 4.28 | 0 | Hydrophobic |
| C21 | CD1 | ILE- 673 | 3.54 | 0 | Hydrophobic |
| C4 | CE | MET- 674 | 4.49 | 0 | Hydrophobic |
| C31 | SD | MET- 674 | 4.12 | 0 | Hydrophobic |
| C17 | CE2 | PHE- 677 | 4.26 | 0 | Hydrophobic |
| C19 | CD2 | PHE- 677 | 3.79 | 0 | Hydrophobic |
| C19 | CG2 | ILE- 682 | 3.9 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 683 | 3.76 | 0 | Hydrophobic |
| C32 | CG2 | ILE- 697 | 3.72 | 0 | Hydrophobic |
| C32 | CG2 | THR- 699 | 3.59 | 0 | Hydrophobic |
| C46 | CE1 | TYR- 701 | 3.7 | 0 | Hydrophobic |
| C48 | CB | MET- 702 | 4.14 | 0 | Hydrophobic |
| C17 | CD2 | LEU- 737 | 4.48 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 737 | 4.32 | 0 | Hydrophobic |
| C17 | CE2 | TYR- 742 | 3.52 | 0 | Hydrophobic |
| C48 | CD2 | LEU- 753 | 4.09 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 753 | 3.88 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 762 | 4 | 0 | Hydrophobic |
| C8 | CB | SER- 763 | 4.33 | 0 | Hydrophobic |
| O1 | N | ASP- 764 | 2.93 | 158.34 | H-Bond (Protein Donor) |
| C24 | CB | ASP- 764 | 3.99 | 0 | Hydrophobic |
| C42 | CE1 | PHE- 765 | 3.46 | 0 | Hydrophobic |
| C7 | CD1 | PHE- 765 | 3.35 | 0 | Hydrophobic |
| C8 | CB | PHE- 765 | 3.78 | 0 | Hydrophobic |
| C24 | CB | LEU- 767 | 4.19 | 0 | Hydrophobic |
| C25 | CD2 | LEU- 767 | 3.94 | 0 | Hydrophobic |
| C23 | CD2 | LEU- 767 | 3.64 | 0 | Hydrophobic |
| C8 | CB | SER- 768 | 4.39 | 0 | Hydrophobic |
| C24 | CB | SER- 768 | 4.27 | 0 | Hydrophobic |
| N44 | O | HOH- 1220 | 2.94 | 155.75 | H-Bond (Ligand Donor) |
