MolNFT v1 · #64338 · protein
Kit kinase domain mutant D816H in complex with sunitinib
3G0F · MAST/STEM cell growth factor receptor: “Kit kinase domain mutant D816H in complex with sunitinib”. X-ray diffraction, 2 ligands (B49, SO4), 6 pockets (best druggability 0.63). MolNFT v1 #64338 on GenesisL1: 3D structure, binding…
- PDB
- 3G0F
- Type
- protein
- Length
- 584 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MAST/STEM cell growth factor receptor
- EC
- 2.7.10.1
- UniProt
- P10721
- Ligands
- B49, SO4
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MAST/STEM cell growth factor receptor (EC 2.7.10.1) | protein | 291 | 36% helix, 20% strand | P10721 |
| B | MAST/STEM cell growth factor receptor (EC 2.7.10.1) | protein | 293 | 38% helix, 22% strand | P10721 |
Ligands and binding sites
- B49 · N-[2-(diethylamino)ethyl]-5-[(Z)-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-3-carboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.63 | 0.85 | 29 | B49 |
| 2 | 143 | 0.62 | 0.85 | 27 | B49 |
| 3 | 258 | 0.56 | 0.77 | 24 | empty |
| 4 | 198 | 0.56 | 0.79 | 42 | empty |
| 5 | 256 | 0.54 | 0.76 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1756 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 3G0F · KIT kinase domain mutant D816H in complex with sunitinib · 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 0.95
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 3G0F · PDBe 3G0F · UniProt P10721
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