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Crystal structure of human C-kit kinase domain in complex with AZD3229-analogue (compound 23)
Analyse Crystal structure of human C-kit kinase domain in complex with AZD3229-analogue… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GQK
- Type
- protein
- Length
- 598 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MAST/STEM cell growth factor receptor kit
- EC
- 2.7.10.1
- UniProt
- P10721
- Ligands
- F88
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MAST/STEM cell growth factor receptor kit (EC 2.7.10.1) | protein | 305 | 43% helix, 18% strand | P10721 |
| B | MAST/STEM cell growth factor receptor kit (EC 2.7.10.1) | protein | 293 | 44% helix, 18% strand | P10721 |
Ligands and binding sites
- F88 · ~{N}-[4-(6,7-dimethoxyquinazolin-4-yl)oxyphenyl]-2-(1-ethylpyrazol-4-yl)ethanamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.81 | 0.88 | 56 | F88 |
| 2 | 288 | 0.76 | 0.88 | 31 | F88 |
| 3 | 402 | 0.75 | 0.85 | 51 | empty |
| 4 | 217 | 0.64 | 0.83 | 35 | empty |
| 5 | 57 | 0.37 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1039 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6GQK · Crystal structure of human c-KIT kinase domain in complex with AZD3229-analogue (compound… · the same entry in another collection · chain A against A, TM-score 1.00
- P10721 · AlphaFold monomer V2.0 prediction for MAST/STEM cell growth factor receptor kit (P10721) · a predicted model of the same protein · chain B against A, TM-score 0.96
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P10721
- Elsewhere: RCSB PDB 6GQK · PDBe 6GQK · UniProt P10721
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