Research workbench
Crystal structure of KIT1 in complex with DP2976 via co-crystallization
Analyse Crystal structure of KIT1 in complex with DP2976 via co-crystallization in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MOB
- Type
- protein
- Length
- 306 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Homo sapiens
- Molecule
- Mast/stem cell growth factor receptor Kit
- EC
- 2.7.10.1
- UniProt
- P10721
- Ligands
- JWY, NO3
- Pockets
- 1 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.8 · 1 distinct chain · 39% 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 | 306 | 39% helix, 18% strand | P10721 |
Ligands and binding sites
- JWY · N-{4-chloro-5-[1-ethyl-7-(methylamino)-2-oxo-1,2-dihydro-1,6-naphthyridin-3-yl]-2-fluorophenyl}-N'-phenylurea · ligand · chains A
- NO3 · Nitrate ion · ion · 14 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.77 | 0.79 | 72 | NO3, JWY |
Compared structures
- 6MOB · Crystal structure of KIT1 in complex with DP2976 via co- crystallization · 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 6MOB · PDBe 6MOB · UniProt P10721
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