Research workbench
FGFR1 in complex with ponatinib.
Analyse FGFR1 in complex with ponatinib. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4V04
- Type
- protein
- Length
- 581 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibroblast growth factor receptor 1 (fms-related tyrosine kinase 2, pfeiffer syndrome)…
- UniProt
- D3DSX2
- Ligands
- 0LI, SO4
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fibroblast growth factor receptor 1 (fms-related tyrosine kinase 2, pfeiffer syndrome), isoform CRA_B | protein | 292 | 38% helix, 15% strand | D3DSX2 |
| B | Fibroblast growth factor receptor 1 (fms-related tyrosine kinase 2, pfeiffer syndrome), isoform CRA_B | protein | 289 | 38% helix, 16% strand | D3DSX2 |
Ligands and binding sites
- 0LI · 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl) phenyl}benzamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.76 | 0.79 | 88 | SO4 |
| 2 | 607 | 0.73 | 0.80 | 67 | 0LI, SO4 |
| 3 | 477 | 0.71 | 0.80 | 65 | EDO, 0LI, SO4 |
| 4 | 96 | 0.37 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 687 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4V04 · FGFR1 in complex with ponatinib. · the same entry in another collection · chain A against A, TM-score 1.00
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 D3DSX2
- Elsewhere: RCSB PDB 4V04 · PDBe 4V04 · UniProt D3DSX2
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