MolNFT v1 · #111290 · protein
(R)-2-phenylpyrrolidine substitute imidazopyridazines: a new class of potent and selective pan-trk inhibitors
4YMJ · Nt-3 growth factor receptor: “(R)-2-phenylpyrrolidine substitute imidazopyridazines: a new class of potent and selective pan-trk inhibitors”. X-ray diffraction, 2 ligands (4EJ, CL), 3 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 4YMJ
- Type
- protein
- Length
- 547 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nt-3 growth factor receptor
- EC
- 2.7.10.1
- UniProt
- Q16288
- Ligands
- 4EJ, CL
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nt-3 growth factor receptor (EC 2.7.10.1) | protein | 271 | 43% helix, 18% strand | Q16288 |
| B | Nt-3 growth factor receptor (EC 2.7.10.1) | protein | 276 | 43% helix, 18% strand | Q16288 |
Ligands and binding sites
- 4EJ · 4-[6-(benzylamino)imidazo[1,2-b]pyridazin-3-yl]benzonitrile · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 6 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 684 | 0.74 | 0.80 | 56 | 4EJ, GOL |
| 2 | 655 | 0.74 | 0.80 | 57 | 4EJ, GOL |
| 3 | 91 | 0.39 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 743 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4YMJ · (R)-2-Phenylpyrrolidine Substitute Imidazopyridazines: a New Class of Potent and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q16288 · AlphaFold monomer V2.0 prediction for nt-3 growth factor receptor (Q16288) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q16288
- Elsewhere: RCSB PDB 4YMJ · PDBe 4YMJ · UniProt Q16288
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