MolNFT v1 · #179837 · protein
Crystal structure of kit kinase domain with a small molecule inhibitor, PLX8512 in the dfg-in state
7KHJ · MAST/STEM cell growth factor receptor kit: “Crystal structure of kit kinase domain with a small molecule inhibitor, PLX8512 in the dfg-in state”. X-ray diffraction, 1 ligand (WEG), 4 pockets (best druggability 0.69). MolNFT v1…
- PDB
- 7KHJ
- Type
- protein
- Length
- 549 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MAST/STEM cell growth factor receptor kit
- Ligands
- WEG
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MAST/STEM cell growth factor receptor kit | protein | 288 | 39% helix, 19% strand | — |
| B | MAST/STEM cell growth factor receptor kit | protein | 261 | 42% helix, 20% strand | — |
Ligands and binding sites
- WEG · 2-phenyl-5-(1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.69 | 0.82 | 50 | empty |
| 2 | 382 | 0.66 | 0.79 | 42 | WEG |
| 3 | 315 | 0.60 | 0.78 | 39 | WEG |
| 4 | 67 | 0.31 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 827 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7KHJ · Crystal structure of KIT kinase domain with a small molecule inhibitor, PLX8512 in the… · 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 7KHJ · PDBe 7KHJ
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