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
2014-07-11
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 23.363 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 43 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.859 | 580.500 |
| % Hydrophobic | % Polar |
|---|---|
| 51.74 | 48.26 |
| According to VolSite | |
| HET Code: | 0LI |
|---|---|
| Formula: | C29H29F3N6O |
| Molecular weight: | 534.575 g/mol |
| DrugBank ID: | DB08901 |
| Buried Surface Area: | 69.28 % |
| Polar Surface area: | 68.22 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 35.3194 | 9.67323 | 45.752 |
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 |
| C11 | CG1 | VAL- 603 | 4.28 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 603 | 4.08 | 0 | Hydrophobic |
| C11 | CB | ALA- 621 | 3.85 | 0 | Hydrophobic |
| C3 | CB | ALA- 621 | 3.67 | 0 | Hydrophobic |
| C8 | CD | LYS- 623 | 4.47 | 0 | Hydrophobic |
| C7 | CB | LYS- 623 | 3.6 | 0 | Hydrophobic |
| N2 | OE1 | GLU- 640 | 2.65 | 157.5 | H-Bond (Ligand Donor) |
| C14 | CG | GLU- 640 | 3.51 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 644 | 4.11 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 644 | 3.81 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 647 | 4.48 | 0 | Hydrophobic |
| F2 | CG2 | ILE- 653 | 3.59 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 654 | 4.36 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 654 | 4.39 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 654 | 4.3 | 0 | Hydrophobic |
| F2 | CG1 | VAL- 654 | 3.93 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 668 | 3.96 | 0 | Hydrophobic |
| C11 | CG2 | THR- 670 | 3.93 | 0 | Hydrophobic |
| C7 | CG2 | THR- 670 | 3.43 | 0 | Hydrophobic |
| N1 | N | CYS- 673 | 2.74 | 170.88 | H-Bond (Protein Donor) |
| F1 | CD2 | LEU- 783 | 4.02 | 0 | Hydrophobic |
| F3 | CD1 | LEU- 783 | 4.03 | 0 | Hydrophobic |
| N4 | O | ILE- 789 | 3.02 | 131.08 | H-Bond (Ligand Donor) |
| N4 | O | HIS- 790 | 2.97 | 126.69 | H-Bond (Ligand Donor) |
| C3 | CD1 | LEU- 799 | 3.73 | 0 | Hydrophobic |
| F1 | CG2 | ILE- 808 | 3.68 | 0 | Hydrophobic |
| F2 | CG2 | ILE- 808 | 4.15 | 0 | Hydrophobic |
| C10 | CB | CYS- 809 | 4.4 | 0 | Hydrophobic |
| O1 | N | ASP- 810 | 2.86 | 160.95 | H-Bond (Protein Donor) |
| C18 | CB | ASP- 810 | 4.05 | 0 | Hydrophobic |
