Research workbench
Crystal structure of kit kinase domain with a small molecule inhibitor, PLX9486 (bezuclastinib) in the dfg-in state
Analyse Crystal structure of kit kinase domain with a small molecule inhibitor, PLX9486… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KHK
- Type
- protein
- Length
- 557 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MAST/STEM cell growth factor receptor kit
- Ligands
- WEJ
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MAST/STEM cell growth factor receptor kit | protein | 291 | 39% helix, 19% strand | — |
| B | MAST/STEM cell growth factor receptor kit | protein | 266 | 41% helix, 17% strand | — |
Ligands and binding sites
- WEJ · 4,5-dimethyl-N-(2-phenyl-1H-pyrrolo[2,3-b]pyridin-5-yl)-1H-pyrazole-3-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.74 | 0.86 | 47 | empty |
| 2 | 432 | 0.65 | 0.78 | 56 | WEJ |
| 3 | 433 | 0.65 | 0.78 | 53 | WEJ |
| 4 | 73 | 0.34 | 0.76 | 21 | empty |
| 5 | 54 | 0.33 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 951 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7KHK · Crystal structure of KIT kinase domain with a small molecule inhibitor, PLX9486… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 7KHK · PDBe 7KHK
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