sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2012-11-06
| 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: | 24.390 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.033 | 310.500 |
| % Hydrophobic | % Polar |
|---|---|
| 63.04 | 36.96 |
| According to VolSite | |
| HET Code: | 647 |
|---|---|
| Formula: | C21H17F3N4 |
| Molecular weight: | 382.382 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 76.64 % |
| Polar Surface area: | 53.6 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 16.5881 | -3.05946 | 9.23168 |
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 |
| C38 | CZ3 | TRP- 557 | 3.33 | 0 | Hydrophobic |
| F45 | CZ3 | TRP- 557 | 3.4 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 595 | 3.73 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 603 | 4.41 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 603 | 3.82 | 0 | Hydrophobic |
| C25 | CG2 | VAL- 603 | 3.9 | 0 | Hydrophobic |
| C13 | CB | ALA- 621 | 4.27 | 0 | Hydrophobic |
| C23 | CB | LYS- 623 | 4.36 | 0 | Hydrophobic |
| C33 | CD2 | LEU- 644 | 3.98 | 0 | Hydrophobic |
| F44 | CD1 | LEU- 647 | 3.7 | 0 | Hydrophobic |
| F43 | CG2 | ILE- 653 | 3.4 | 0 | Hydrophobic |
| F44 | CB | ILE- 653 | 3.65 | 0 | Hydrophobic |
| C33 | CB | VAL- 654 | 4.4 | 0 | Hydrophobic |
| C23 | CG2 | THR- 670 | 3.93 | 0 | Hydrophobic |
| N8 | O | GLU- 671 | 2.93 | 158.14 | H-Bond (Ligand Donor) |
| N5 | N | CYS- 673 | 2.88 | 153.73 | H-Bond (Protein Donor) |
| F44 | CD1 | LEU- 783 | 3.81 | 0 | Hydrophobic |
| F45 | CD2 | LEU- 783 | 3.37 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 799 | 3.39 | 0 | Hydrophobic |
| F43 | CB | ILE- 808 | 3.25 | 0 | Hydrophobic |
| F45 | CG2 | ILE- 808 | 4.03 | 0 | Hydrophobic |
| C33 | CB | CYS- 809 | 4.39 | 0 | Hydrophobic |
| N21 | N | ASP- 810 | 3.25 | 154.61 | H-Bond (Protein Donor) |
| C29 | CB | ASP- 810 | 4.49 | 0 | Hydrophobic |
| C40 | CB | ASP- 810 | 3.76 | 0 | Hydrophobic |
| C15 | CE1 | PHE- 811 | 3.89 | 0 | Hydrophobic |
