Research workbench
FGFR1 complex with N-(2-((5-((2,6-dichloro-3,5-DIMETHOXYBENZYL)OXY) pyrimidin-2-YL)AMINO)-3-METHYLPHENYL)ACRYLAMIDE
Analyse FGFR1 complex with N-(2-((5-((2,6-dichloro-3,5-DIMETHOXYBENZYL)OXY)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NVL
- Type
- protein
- Length
- 1,077 residues
- Chains
- 4
- 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
- XL6, SO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fibroblast growth factor receptor 1 (EC 2.7.10.1) | protein | 280 | 40% helix, 15% strand | P11362 |
| B | Fibroblast growth factor receptor 1 (EC 2.7.10.1) | protein | 263 | 42% helix, 14% strand | P11362 |
| C | Fibroblast growth factor receptor 1 (EC 2.7.10.1) | protein | 265 | 44% helix, 15% strand | P11362 |
| D | Fibroblast growth factor receptor 1 (EC 2.7.10.1) | protein | 269 | 41% helix, 13% strand | P11362 |
Ligands and binding sites
- XL6 · N-[2-({5-[(2,6-dichloro-3,5-dimethoxyphenyl) methoxy]pyrimidin-2-yl}amino)-3-methylphenyl]propanamide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 622 | 0.78 | 0.83 | 68 | empty |
| 2 | 364 | 0.70 | 0.83 | 45 | empty |
| 3 | 286 | 0.68 | 0.83 | 37 | XL6 |
| 4 | 139 | 0.60 | 0.84 | 25 | XL6 |
| 5 | 214 | 0.59 | 0.80 | 29 | XL6 |
Interfaces
5 interfaces between chains.
- A–B · 699 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 305 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 292 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 286 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 28 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6NVL · FGFR1 complex with N-(2-((5-((2,6-dichloro-3,5-dimethoxybenzyl)oxy)pyrimidin-2-yl)amino)-3… · the same entry in another collection · chain D against D, 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 0.94
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 P11362
- Elsewhere: RCSB PDB 6NVL · PDBe 6NVL · UniProt P11362
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