sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.250 Å
X-ray
2006-06-16
| 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: | 36.311 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.210 | 367.875 |
| % Hydrophobic | % Polar |
|---|---|
| 63.30 | 36.70 |
| According to VolSite | |
| HET Code: | PP1 |
|---|---|
| Formula: | C16H19N5 |
| Molecular weight: | 281.356 g/mol |
| DrugBank ID: | DB01809 |
| Buried Surface Area: | 67.42 % |
| Polar Surface area: | 69.62 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 24.2373 | 7.09786 | 10.1952 |
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 |
| C37 | CB | LEU- 730 | 3.73 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 738 | 4.15 | 0 | Hydrophobic |
| C37 | CB | VAL- 738 | 4.17 | 0 | Hydrophobic |
| C16 | CG2 | VAL- 738 | 3.86 | 0 | Hydrophobic |
| C5 | CB | ALA- 756 | 4.12 | 0 | Hydrophobic |
| C16 | CB | ALA- 756 | 4.08 | 0 | Hydrophobic |
| C15 | CB | LYS- 758 | 3.78 | 0 | Hydrophobic |
| C24 | CG | GLU- 775 | 4.24 | 0 | Hydrophobic |
| C24 | CD1 | LEU- 779 | 4.01 | 0 | Hydrophobic |
| C24 | CD1 | LEU- 802 | 4.25 | 0 | Hydrophobic |
| C24 | CG1 | VAL- 804 | 3.64 | 0 | Hydrophobic |
| C16 | CG2 | VAL- 804 | 3.58 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 804 | 3.22 | 0 | Hydrophobic |
| N10 | O | GLU- 805 | 2.87 | 152.26 | H-Bond (Ligand Donor) |
| N7 | N | ALA- 807 | 3.13 | 165.47 | H-Bond (Protein Donor) |
| C29 | CB | SER- 811 | 4.02 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 881 | 3.57 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 881 | 4.19 | 0 | Hydrophobic |
| C29 | CD2 | LEU- 881 | 3.64 | 0 | Hydrophobic |
