Research workbench
The crystal structure of FGFR4 kinase domain in complex with N-(5- cyano-4-((2-METHOXYETHYL)AMINO)PYRIDIN-2-yl)-7-(2,2,2- trifluoroacetyl)-3,4-dihydro-1,8-naphthyridine-1(2H)-carboxamide
Analyse The crystal structure of FGFR4 kinase domain in complex with N-(5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VJL
- Type
- protein
- Length
- 529 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibroblast growth factor receptor 4
- EC
- 2.7.10.1
- UniProt
- P22455
- Ligands
- 7IF
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fibroblast growth factor receptor 4 (EC 2.7.10.1) | protein | 263 | 40% helix, 16% strand | P22455 |
| B | Fibroblast growth factor receptor 4 (EC 2.7.10.1) | protein | 266 | 42% helix, 16% strand | P22455 |
Ligands and binding sites
- 7IF · N-[5-(aminomethyl)-4-(2-methoxyethylamino)pyridin-2-yl]-7-[2,2,2-tris(fluoranyl)ethanoyl]-3,4-dihydro-2H-1,8-naphthyridine-1-carboxamide · ligand · 2 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.52 | 0.76 | 34 | 7IF |
| 2 | 110 | 0.45 | 0.78 | 27 | 7IF |
| 3 | 64 | 0.29 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 99 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7VJL · The crystal structure of FGFR4 kinase domain in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P22455 · AlphaFold monomer V2.0 prediction for fibroblast growth factor receptor 4 (P22455) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P22455
- Elsewhere: RCSB PDB 7VJL · PDBe 7VJL · UniProt P22455
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