Research workbench
Crystal structure of kit kinase domain with a small molecule inhibitor, PLX647
Analyse Crystal structure of kit kinase domain with a small molecule inhibitor, PLX647 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HVS
- Type
- protein
- Length
- 326 residues
- Chains
- 1
- 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
- 647
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MAST/STEM cell growth factor receptor kit (EC 2.7.10.1) | protein | 326 | 41% helix, 20% strand | P10721 |
Ligands and binding sites
- 647 · 5-(1H-pyrrolo[2,3-b]pyridin-3-ylmethyl)-N-[4-(trifluoromethyl)benzyl]pyridin-2-amine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.79 | 0.92 | 37 | 647 |
| 2 | 65 | 0.33 | 0.76 | 19 | empty |
| 3 | 67 | 0.28 | 0.73 | 15 | empty |
Compared structures
- 4HVS · Crystal structure of KIT kinase domain with a small molecule inhibitor, PLX647 · 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 4HVS · PDBe 4HVS · UniProt P10721
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