MolNFT v1 · #137398 · protein
Crystal structure of FGFR1-Y563C (FGFR4 surrogate) covalently bound to H3B-6527
5VND · Fibroblast growth factor receptor 1: “Crystal structure of FGFR1-Y563C (FGFR4 surrogate) covalently bound to H3B-6527”. X-ray diffraction, 2 ligands (9ES, SO4), 4 pockets (best druggability 0.78). MolNFT v1 #137398 on GenesisL1: 3D…
- PDB
- 5VND
- Type
- protein
- Length
- 597 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibroblast growth factor receptor 1
- EC
- 2.7.10.1
- UniProt
- P11362
- Ligands
- 9ES, SO4
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fibroblast growth factor receptor 1 (EC 2.7.10.1) | protein | 302 | 36% helix, 15% strand | P11362 |
| B | Fibroblast growth factor receptor 1 (EC 2.7.10.1) | protein | 295 | 37% helix, 16% strand | P11362 |
Ligands and binding sites
- 9ES · N-{2-[(6-{[(2,6-dichloro-3,5-dimethoxyphenyl) carbamoyl](methyl)amino}pyrimidin-4-yl)amino]-5-(4-ethylpiperazin-1-yl)phenyl}propanamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 15 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 | 1200 | 0.78 | 0.79 | 91 | SO4, EDO |
| 2 | 815 | 0.74 | 0.79 | 70 | 9ES, SO4, EDO |
| 3 | 845 | 0.73 | 0.78 | 67 | 9ES, SO4 |
| 4 | 126 | 0.44 | 0.77 | 21 | EDO |
Interfaces
1 interface between chains.
- A–B · 737 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5VND · Crystal structure of FGFR1-Y563C (FGFR4 surrogate) covalently bound to H3B-6527 · the same entry in another collection · chain A against A, TM-score 1.00
- P11362 · AlphaFold monomer V2.0 prediction for fibroblast growth factor receptor 1 (P11362) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 P11362
- Elsewhere: RCSB PDB 5VND · PDBe 5VND · UniProt P11362
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