sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2010-01-13
| 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: | 34.892 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.090 | 678.375 |
| % Hydrophobic | % Polar |
|---|---|
| 52.24 | 47.76 |
| According to VolSite | |
| HET Code: | X2L |
|---|---|
| Formula: | C16H14N2O2 |
| Molecular weight: | 266.295 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.45 % |
| Polar Surface area: | 64.34 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -11.414 | -26.1056 | 11.2582 |
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 |
| CAH | CB | LEU- 730 | 3.71 | 0 | Hydrophobic |
| CAM | CD2 | LEU- 730 | 4.23 | 0 | Hydrophobic |
| CAQ | CD1 | LEU- 730 | 3.71 | 0 | Hydrophobic |
| CAJ | CG1 | VAL- 738 | 4.45 | 0 | Hydrophobic |
| CAU | CG1 | VAL- 738 | 3.62 | 0 | Hydrophobic |
| CAN | CG2 | VAL- 738 | 3.58 | 0 | Hydrophobic |
| CAJ | CB | ALA- 756 | 4.45 | 0 | Hydrophobic |
| CAG | CD | LYS- 758 | 4.42 | 0 | Hydrophobic |
| CAJ | CG2 | VAL- 804 | 3.67 | 0 | Hydrophobic |
| NAL | O | GLU- 805 | 3 | 174.55 | H-Bond (Ligand Donor) |
| OAA | N | ALA- 807 | 2.77 | 175.52 | H-Bond (Protein Donor) |
| CAU | CD2 | LEU- 881 | 3.54 | 0 | Hydrophobic |
| CAJ | CD1 | LEU- 881 | 3.56 | 0 | Hydrophobic |
| CAG | CB | SER- 891 | 4.31 | 0 | Hydrophobic |
| NAB | OD1 | ASP- 892 | 3.3 | 132.82 | H-Bond (Ligand Donor) |
