Research workbench
Crystal structure of TRKc in complex with 3-((6-(4-aminophenyl)imidazo[1,2-a]pyrazin-3-yl)ethynyl)- N-(3-isopropyl-5-((4-methylpiperazin-1-yl)methyl)phenyl)-2- methylbenzamide
Analyse Crystal structure of TRKc in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KZD
- Type
- protein
- Length
- 282 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.708
- Source
- Homo sapiens
- Molecule
- NT-3 growth factor receptor
- EC
- 2.7.10.1
- UniProt
- Q16288
- Ligands
- DZ6, PO4
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · resolution 1.708 · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NT-3 growth factor receptor (EC 2.7.10.1) | protein | 282 | 39% helix, 18% strand | Q16288 |
Ligands and binding sites
- DZ6 · 3-[2-[6-(4-aminophenyl)imidazo[1,2-a]pyrazin-3-yl]ethynyl]-2-methyl-~{N}-[3-(4-methylpiperazin-1-yl)-5-propan-2-yl-phenyl]benzamide · ligand · chains A
- PO4 · Phosphate 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.75 | 0.79 | 72 | DZ6 |
| 2 | 111 | 0.44 | 0.78 | 25 | empty |
| 3 | 54 | 0.29 | 0.75 | 15 | empty |
Compared structures
- 6KZD · Crystal structure of trkc in complex with 3-((6-(4-aminophenyl)… · 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 0.95
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 Q16288
- Elsewhere: RCSB PDB 6KZD · PDBe 6KZD · UniProt Q16288
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