Research workbench
The cocrystal structure of FGFR2 bound with compound 14 harboring 5H- PYRROLO[2,3-B]PYRAZINE scaffold
Analyse The cocrystal structure of FGFR2 bound with compound 14 harboring 5H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AGX
- Type
- protein
- Length
- 1,165 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibroblast growth factor receptor 2
- EC
- 2.7.10.1
- UniProt
- P21802
- Ligands
- 9WX
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fibroblast growth factor receptor 2 (EC 2.7.10.1) | protein | 285 | 36% helix, 18% strand | P21802 |
| B, D | Fibroblast growth factor receptor 2 (EC 2.7.10.1) | protein | 298 | 36% helix, 18% strand | P21802 |
| C | Fibroblast growth factor receptor 2 (EC 2.7.10.1) | protein | 284 | 37% helix, 18% strand | P21802 |
Ligands and binding sites
- 9WX · ethyl [4-({3-[2-(3,5-dimethoxyphenyl)ethyl]-5H-pyrrolo[2,3-b]pyrazin-5-yl}sulfonyl)-1H-imidazol-1-yl]acetate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.85 | 0.86 | 101 | 9WX |
| 2 | 699 | 0.78 | 0.83 | 60 | 9WX |
| 3 | 705 | 0.78 | 0.83 | 62 | 9WX |
| 4 | 356 | 0.56 | 0.74 | 39 | empty |
| 5 | 202 | 0.46 | 0.74 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1451 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1444 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 373 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (phosphorylation).
Compared structures
- 6AGX · The cocrystal structure of FGFR2 bound with compound 14 harboring… · the same entry in another collection · chain B against B, TM-score 1.00
- P21802 · AlphaFold monomer V2.0 prediction for fibroblast growth factor receptor 2 (P21802) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P21802
- Elsewhere: RCSB PDB 6AGX · PDBe 6AGX · UniProt P21802
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