Research workbench
Crystal structure of the kinase domain of human C-kit in complex with a type-II inhibitor bearing an acrylamide
Analyse Crystal structure of the kinase domain of human C-kit in complex with a type-II… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XVA
- Type
- protein
- Length
- 582 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MAST/STEM cell growth factor receptor KIT,MAST/STEM cell growth factor receptor kit
- EC
- 2.7.10.1
- UniProt
- P10721
- Ligands
- O2K
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MAST/STEM cell growth factor receptor KIT,MAST/STEM cell growth factor receptor kit (EC 2.7.10.1) | protein | 294 | 42% helix, 18% strand | P10721 |
| B | MAST/STEM cell growth factor receptor KIT,MAST/STEM cell growth factor receptor kit (EC 2.7.10.1) | protein | 288 | 42% helix, 18% strand | P10721 |
Ligands and binding sites
- O2K · ~{N}-[[3-[2-[3-methoxy-5-(7-methoxyquinolin-4-yl)oxy-pyridin-2-yl]ethanoylamino]-5-methyl-phenyl]methyl]propanamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.78 | 0.83 | 86 | O2K |
| 2 | 531 | 0.78 | 0.85 | 54 | O2K |
| 3 | 362 | 0.72 | 0.84 | 51 | empty |
Interfaces
1 interface between chains.
- A–B · 853 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6XVA · Crystal structure of the kinase domain of human c-KIT in complex with a type-II inhibitor… · 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 A against A, TM-score 0.97
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 6XVA · PDBe 6XVA · UniProt P10721
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.