sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2009-01-27
| Name: | Mast/stem cell growth factor receptor Kit |
|---|---|
| ID: | KIT_HUMAN |
| AC: | P10721 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.10.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 44.563 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.269 | 691.875 |
| % Hydrophobic | % Polar |
|---|---|
| 57.07 | 42.93 |
| According to VolSite | |
| HET Code: | B49 |
|---|---|
| Formula: | C22H28FN4O2 |
| Molecular weight: | 399.482 g/mol |
| DrugBank ID: | DB01268 |
| Buried Surface Area: | 61.67 % |
| Polar Surface area: | 78.43 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -19.759 | 126.247 | -18.4737 |
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 |
| C4 | CD2 | LEU- 595 | 4.04 | 0 | Hydrophobic |
| C3 | CB | LEU- 595 | 4.38 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 603 | 4.45 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 603 | 3.88 | 0 | Hydrophobic |
| F29 | CG2 | VAL- 603 | 3.41 | 0 | Hydrophobic |
| C6 | CB | ALA- 621 | 4.07 | 0 | Hydrophobic |
| F29 | CD | LYS- 623 | 4.1 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 654 | 4.07 | 0 | Hydrophobic |
| N24 | O | GLU- 671 | 3.02 | 177.25 | H-Bond (Ligand Donor) |
| C4 | CE1 | TYR- 672 | 3.67 | 0 | Hydrophobic |
| O27 | N | CYS- 673 | 2.87 | 172.41 | H-Bond (Protein Donor) |
| C6 | CD1 | LEU- 799 | 4.35 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 799 | 3.6 | 0 | Hydrophobic |
| C5 | SG | CYS- 809 | 3.41 | 0 | Hydrophobic |
| C7 | SG | CYS- 809 | 3.95 | 0 | Hydrophobic |
| C5 | SG | CYS- 809 | 3.41 | 0 | Hydrophobic |
| C3 | CZ | PHE- 811 | 4.21 | 0 | Hydrophobic |
| F29 | CG | PHE- 811 | 3.69 | 0 | Hydrophobic |
