sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2012-07-12
| 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: | 25.409 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.429 | 475.875 |
| % Hydrophobic | % Polar |
|---|---|
| 51.77 | 48.23 |
| According to VolSite | |
| HET Code: | C07 |
|---|---|
| Formula: | C18H18N4O2 |
| Molecular weight: | 322.361 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.19 % |
| Polar Surface area: | 92.34 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| -8.98787 | 8.00154 | 51.4859 |
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 |
| C10 | CG1 | VAL- 627 | 4.34 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 635 | 4.31 | 0 | Hydrophobic |
| C | CG1 | VAL- 635 | 4.06 | 0 | Hydrophobic |
| C14 | CB | ALA- 651 | 4.04 | 0 | Hydrophobic |
| C | CB | ALA- 651 | 3.53 | 0 | Hydrophobic |
| DuAr | NZ | LYS- 653 | 3.82 | 26.72 | Pi/Cation |
| C6 | CD | LYS- 653 | 3.46 | 0 | Hydrophobic |
| C1 | CG | LYS- 653 | 3.58 | 0 | Hydrophobic |
| O | OE2 | GLU- 670 | 2.51 | 141.61 | H-Bond (Ligand Donor) |
| C5 | SD | MET- 674 | 3.83 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 697 | 4.35 | 0 | Hydrophobic |
| N3 | OG1 | THR- 699 | 3.14 | 135.16 | H-Bond (Protein Donor) |
| C6 | CG2 | THR- 699 | 3.48 | 0 | Hydrophobic |
| N2 | N | MET- 702 | 3.16 | 133.38 | H-Bond (Protein Donor) |
| N1 | O | MET- 702 | 3.01 | 143.27 | H-Bond (Ligand Donor) |
| C14 | CD1 | LEU- 753 | 3.63 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 753 | 4.43 | 0 | Hydrophobic |
| C3 | CB | SER- 763 | 4.41 | 0 | Hydrophobic |
| O | N | ASP- 764 | 3 | 146.41 | H-Bond (Protein Donor) |
