Research workbench
Crystal structure of JAK3 in complex with compound 10 (FM475)
Analyse Crystal structure of JAK3 in complex with compound 10 (FM475) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GL9
- Type
- protein
- Length
- 583 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase JAK3
- EC
- 2.7.10.2
- UniProt
- P52333
- Ligands
- F3W, PHU
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase JAK3 (EC 2.7.10.2) | protein | 292 | 43% helix, 19% strand | P52333 |
| B | Tyrosine-protein kinase JAK3 (EC 2.7.10.2) | protein | 291 | 44% helix, 20% strand | P52333 |
Ligands and binding sites
- F3W · (~{E})-3-[3-(3-cyclohexyl-3,5,8,10-tetrazatricyclo[7.3.0.0^{2,6}]dodeca-1(9),2(6),4,7,11-pentaen-4-yl)phenyl]prop-2-enenitrile · ligand · 2 copies · chains A, B
- PHU · 1-phenylurea · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.83 | 0.84 | 101 | F3W, EDO |
| 2 | 68 | 0.74 | 0.98 | 17 | PHU |
| 3 | 69 | 0.74 | 0.97 | 16 | PHU |
| 4 | 625 | 0.72 | 0.79 | 69 | F3W, EDO |
| 5 | 95 | 0.43 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 869 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6GL9 · Crystal structure of JAK3 in complex with Compound 10 (FM475) · the same entry in another collection · chain A against A, TM-score 1.00
- P52333 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase JAK3 (P52333) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P52333
- Elsewhere: RCSB PDB 6GL9 · PDBe 6GL9 · UniProt P52333
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