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
2014-01-06
| Name: | Proto-oncogene tyrosine-protein kinase receptor Ret |
|---|---|
| ID: | RET_HUMAN |
| AC: | P07949 |
| 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: | 31.811 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.898 | 334.125 |
| % Hydrophobic | % Polar |
|---|---|
| 58.59 | 41.41 |
| According to VolSite | |
| HET Code: | ADN |
|---|---|
| Formula: | C10H13N5O4 |
| Molecular weight: | 267.241 g/mol |
| DrugBank ID: | DB00640 |
| Buried Surface Area: | 65.99 % |
| Polar Surface area: | 139.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 26.4922 | 10.7376 | 10.2372 |
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 |
| C1' | CB | LEU- 730 | 3.96 | 0 | Hydrophobic |
| C5' | CG2 | VAL- 738 | 4.46 | 0 | Hydrophobic |
| N6 | O | GLU- 805 | 2.77 | 160.89 | H-Bond (Ligand Donor) |
| N1 | N | ALA- 807 | 2.94 | 169.87 | H-Bond (Protein Donor) |
| C3' | CB | SER- 811 | 4.3 | 0 | Hydrophobic |
| C2' | CD2 | LEU- 881 | 4.15 | 0 | Hydrophobic |
