MolNFT v1 · #81881 · protein
Discovery of a selective trk inhibitor with efficacy in rodent cancer tumor models
3V5Q · Nt-3 growth factor receptor: “Discovery of a selective trk inhibitor with efficacy in rodent cancer tumor models”. X-ray diffraction, 2 ligands (0F4, CL), 3 pockets (best druggability 0.68). MolNFT v1 #81881 on GenesisL1: 3D…
- PDB
- 3V5Q
- Type
- protein
- Length
- 528 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
- 0F4, CL
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nt-3 growth factor receptor (EC 2.7.10.1) | protein | 263 | 44% helix, 16% strand | Q16288 |
| B | Nt-3 growth factor receptor (EC 2.7.10.1) | protein | 265 | 43% helix, 17% strand | Q16288 |
Ligands and binding sites
- 0F4 · 1-(3-{[(3Z)-2-oxo-3-(1H-pyrrol-2-ylmethylidene)-2,3-dihydro-1H-indol-6-yl]amino}phenyl)-3-[3-(trifluoromethyl)phenyl]urea · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.68 | 0.79 | 45 | 0F4 |
| 2 | 462 | 0.67 | 0.79 | 52 | 0F4 |
| 3 | 52 | 0.36 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 689 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3V5Q · Discovery of a selective TRK Inhibitor with efficacy in rodent cancer tumor models · 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 B 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 3V5Q · PDBe 3V5Q · UniProt Q16288
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