MolNFT v1 · #152797 · protein
Crystal structure of unactivated C-kit in complex with compound
6ITT · MAST/STEM cell growth factor receptor kit: “Crystal structure of unactivated C-kit in complex with compound”. X-ray diffraction, 1 ligand (AWO), 8 pockets (best druggability 0.77). MolNFT v1 #152797 on GenesisL1: 3D structure…
- PDB
- 6ITT
- 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
- AWO
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 45% 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 | 301 | 45% helix, 18% strand | P10721 |
| B | MAST/STEM cell growth factor receptor kit (EC 2.7.10.1) | protein | 297 | 44% helix, 18% strand | P10721 |
Ligands and binding sites
- AWO · N-(5-ethyl-1,2-oxazol-3-yl)-N'-[4-(2-{[6-(4-ethylpyrazin-1(4H)-yl)pyrimidin-4-yl]amino}-1,3-thiazol-5-yl)phenyl]urea · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.77 | 0.79 | 86 | AWO |
| 2 | 720 | 0.75 | 0.80 | 65 | AWO |
| 3 | 263 | 0.63 | 0.80 | 31 | empty |
| 4 | 257 | 0.51 | 0.75 | 37 | empty |
| 5 | 87 | 0.38 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 878 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6ITT · Crystal structure of unactivated c-KIT in complex with 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 0.95
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 6ITT · PDBe 6ITT · UniProt P10721
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